diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml index 0663698e6..0b1a152ef 100644 --- a/.github/workflows/test.yml +++ b/.github/workflows/test.yml @@ -90,7 +90,7 @@ jobs: run: | # ran only on certain files for now # add here when checked - poetry run black schematic --check + poetry run black schematic tests schematic_api --check #---------------------------------------------- # type checking/enforcement @@ -101,7 +101,7 @@ jobs: # add here when checked # poetry run mypy --install-types --non-interactive # add here when enforced - poetry run mypy --disallow-untyped-defs --install-types --non-interactive schematic/configuration/*.py schematic/exceptions.py schematic/help.py schematic/loader.py schematic/version.py schematic/visualization schematic/utils/ + poetry run mypy --disallow-untyped-defs --install-types --non-interactive schematic/schemas/ schematic/configuration/ schematic/exceptions.py schematic/help.py schematic/loader.py schematic/version.py schematic/visualization schematic/utils/ #---------------------------------------------- # linting diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index 623446ced..16c72afc9 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -10,4 +10,12 @@ repos: # pre-commit's default_language_version, see # https://pre-commit.com/#top_level-default_language_version language_version: python3.10 - files: schematic/ \ No newline at end of file + files: ^(tests|schematic|schematic_api)/ + + - repo: https://github.com/pycqa/isort + rev: 5.13.2 + hooks: + - id: isort + name: isort (python) + files: ^(tests|schematic|schematic_api)/ + args: ["--profile", "black", "--filter-files"] diff --git a/README.md b/README.md index 228e0e779..3d0bf04ca 100644 --- a/README.md +++ b/README.md @@ -141,8 +141,6 @@ model: # This section is for using google sheets with Schematic google_sheets: - # The Synapse id of the Google service account credentials. - service_acct_creds_synapse_id: "syn25171627" # Path to the synapse config file, either absolute or relative to this file service_acct_creds: "schematic_service_account_creds.json" # When doing google sheet validation (regex match) with the validation rules. diff --git a/config_example.yml b/config_example.yml index 245b8fefe..9125cb6bb 100644 --- a/config_example.yml +++ b/config_example.yml @@ -35,8 +35,6 @@ model: # This section is for using google sheets with Schematic google_sheets: - # The Synapse id of the Google service account credentials. - service_acct_creds_synapse_id: "syn25171627" # Path to the synapse config file, either absolute or relative to this file service_acct_creds: "schematic_service_account_creds.json" # When doing google sheet validation (regex match) with the validation rules. diff --git a/poetry.lock b/poetry.lock index 7314c46cb..203239b7a 100644 --- a/poetry.lock +++ b/poetry.lock @@ -190,6 +190,20 @@ files = [ [package.dependencies] typing-extensions = {version = ">=4.0.0", markers = 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"sha256:e4d936c9de8727928f3be6079590e97d9abfe8d39a590be678eb5919ffc186bb"}, ] [package.dependencies] @@ -4460,28 +4597,28 @@ telegram = ["requests"] [[package]] name = "traitlets" -version = "5.14.1" +version = "5.14.3" description = "Traitlets Python configuration system" optional = false python-versions = ">=3.8" files = [ - {file = "traitlets-5.14.1-py3-none-any.whl", hash = "sha256:2e5a030e6eff91737c643231bfcf04a65b0132078dad75e4936700b213652e74"}, - {file = "traitlets-5.14.1.tar.gz", hash = "sha256:8585105b371a04b8316a43d5ce29c098575c2e477850b62b848b964f1444527e"}, + {file = "traitlets-5.14.3-py3-none-any.whl", hash = "sha256:b74e89e397b1ed28cc831db7aea759ba6640cb3de13090ca145426688ff1ac4f"}, + {file = "traitlets-5.14.3.tar.gz", hash = "sha256:9ed0579d3502c94b4b3732ac120375cda96f923114522847de4b3bb98b96b6b7"}, ] [package.extras] docs = ["myst-parser", "pydata-sphinx-theme", "sphinx"] -test = ["argcomplete (>=3.0.3)", "mypy (>=1.7.0)", "pre-commit", "pytest (>=7.0,<7.5)", "pytest-mock", "pytest-mypy-testing"] +test = ["argcomplete (>=3.0.3)", "mypy (>=1.7.0)", "pre-commit", "pytest (>=7.0,<8.2)", "pytest-mock", "pytest-mypy-testing"] [[package]] name = "types-python-dateutil" -version = "2.8.19.20240106" +version = "2.9.0.20240316" description = "Typing stubs for python-dateutil" optional = false python-versions = ">=3.8" files = [ - {file = "types-python-dateutil-2.8.19.20240106.tar.gz", hash = "sha256:1f8db221c3b98e6ca02ea83a58371b22c374f42ae5bbdf186db9c9a76581459f"}, - {file = "types_python_dateutil-2.8.19.20240106-py3-none-any.whl", hash = "sha256:efbbdc54590d0f16152fa103c9879c7d4a00e82078f6e2cf01769042165acaa2"}, + {file = "types-python-dateutil-2.9.0.20240316.tar.gz", hash = "sha256:5d2f2e240b86905e40944dd787db6da9263f0deabef1076ddaed797351ec0202"}, + {file = "types_python_dateutil-2.9.0.20240316-py3-none-any.whl", hash = "sha256:6b8cb66d960771ce5ff974e9dd45e38facb81718cc1e208b10b1baccbfdbee3b"}, ] [[package]] @@ -4581,12 +4718,12 @@ socks = ["PySocks (>=1.5.6,!=1.5.7,<2.0)"] [[package]] name = "uwsgi" -version = "2.0.24" +version = "2.0.25.1" description = "The uWSGI server" optional = true python-versions = "*" files = [ - {file = "uwsgi-2.0.24.tar.gz", hash = "sha256:77b6dd5cd633f4ae87ee393f7701f617736815499407376e78f3d16467523afe"}, + {file = "uwsgi-2.0.25.1.tar.gz", hash = "sha256:d653d2d804c194c8cbe2585fa56efa2650313ae75c686a9d7931374d4dfbfc6e"}, ] [[package]] @@ -4607,13 +4744,13 @@ test = ["flake8 (>=2.4.0)", "isort (>=4.2.2)", "pytest (>=2.2.3)"] [[package]] name = "virtualenv" -version = "20.25.1" +version = "20.26.1" description = "Virtual Python Environment builder" optional = false python-versions = ">=3.7" files = [ - {file = "virtualenv-20.25.1-py3-none-any.whl", hash = "sha256:961c026ac520bac5f69acb8ea063e8a4f071bcc9457b9c1f28f6b085c511583a"}, - {file = "virtualenv-20.25.1.tar.gz", hash = "sha256:e08e13ecdca7a0bd53798f356d5831434afa5b07b93f0abdf0797b7a06ffe197"}, + {file = "virtualenv-20.26.1-py3-none-any.whl", hash = "sha256:7aa9982a728ae5892558bff6a2839c00b9ed145523ece2274fad6f414690ae75"}, + {file = "virtualenv-20.26.1.tar.gz", hash = "sha256:604bfdceaeece392802e6ae48e69cec49168b9c5f4a44e483963f9242eb0e78b"}, ] [package.dependencies] @@ -4622,7 +4759,7 @@ filelock = ">=3.12.2,<4" platformdirs = ">=3.9.1,<5" [package.extras] -docs = ["furo (>=2023.7.26)", "proselint (>=0.13)", "sphinx (>=7.1.2)", "sphinx-argparse (>=0.4)", "sphinxcontrib-towncrier (>=0.2.1a0)", "towncrier (>=23.6)"] +docs = ["furo (>=2023.7.26)", "proselint (>=0.13)", "sphinx (>=7.1.2,!=7.3)", "sphinx-argparse (>=0.4)", "sphinxcontrib-towncrier (>=0.2.1a0)", "towncrier (>=23.6)"] test = ["covdefaults (>=2.3)", "coverage (>=7.2.7)", "coverage-enable-subprocess (>=1)", "flaky (>=3.7)", "packaging (>=23.1)", "pytest (>=7.4)", "pytest-env (>=0.8.2)", "pytest-freezer (>=0.4.8)", "pytest-mock (>=3.11.1)", "pytest-randomly (>=3.12)", "pytest-timeout (>=2.1)", "setuptools (>=68)", "time-machine (>=2.10)"] [[package]] @@ -4664,17 +4801,17 @@ files = [ [[package]] name = "websocket-client" -version = "1.7.0" +version = "1.8.0" description = "WebSocket client for Python with low level API options" optional = false python-versions = ">=3.8" files = [ - {file = "websocket-client-1.7.0.tar.gz", hash = "sha256:10e511ea3a8c744631d3bd77e61eb17ed09304c413ad42cf6ddfa4c7787e8fe6"}, - {file = "websocket_client-1.7.0-py3-none-any.whl", hash = "sha256:f4c3d22fec12a2461427a29957ff07d35098ee2d976d3ba244e688b8b4057588"}, + {file = "websocket_client-1.8.0-py3-none-any.whl", hash = "sha256:17b44cc997f5c498e809b22cdf2d9c7a9e71c02c8cc2b6c56e7c2d1239bfa526"}, + {file = "websocket_client-1.8.0.tar.gz", hash = "sha256:3239df9f44da632f96012472805d40a23281a991027ce11d2f45a6f24ac4c3da"}, ] [package.extras] -docs = ["Sphinx (>=6.0)", "sphinx-rtd-theme (>=1.1.0)"] +docs = ["Sphinx (>=6.0)", "myst-parser (>=2.0.0)", "sphinx-rtd-theme (>=1.1.0)"] optional = ["python-socks", "wsaccel"] test = ["websockets"] @@ -4787,24 +4924,24 @@ files = [ [[package]] name = "zipp" -version = "3.17.0" +version = "3.18.1" description = "Backport of pathlib-compatible object wrapper for zip files" optional = false python-versions = ">=3.8" files = [ - {file = "zipp-3.17.0-py3-none-any.whl", hash = "sha256:0e923e726174922dce09c53c59ad483ff7bbb8e572e00c7f7c46b88556409f31"}, - {file = "zipp-3.17.0.tar.gz", hash = "sha256:84e64a1c28cf7e91ed2078bb8cc8c259cb19b76942096c8d7b84947690cabaf0"}, + {file = "zipp-3.18.1-py3-none-any.whl", hash = "sha256:206f5a15f2af3dbaee80769fb7dc6f249695e940acca08dfb2a4769fe61e538b"}, + {file = "zipp-3.18.1.tar.gz", hash = "sha256:2884ed22e7d8961de1c9a05142eb69a247f120291bc0206a00a7642f09b5b715"}, ] [package.extras] -docs = ["furo", "jaraco.packaging (>=9.3)", "jaraco.tidelift (>=1.4)", "rst.linker (>=1.9)", "sphinx (<7.2.5)", "sphinx (>=3.5)", "sphinx-lint"] -testing = ["big-O", "jaraco.functools", "jaraco.itertools", "more-itertools", "pytest (>=6)", "pytest-black (>=0.3.7)", "pytest-checkdocs (>=2.4)", "pytest-cov", "pytest-enabler (>=2.2)", "pytest-ignore-flaky", "pytest-mypy (>=0.9.1)", "pytest-ruff"] +docs = ["furo", "jaraco.packaging (>=9.3)", "jaraco.tidelift (>=1.4)", "rst.linker (>=1.9)", "sphinx (>=3.5)", "sphinx-lint"] +testing = ["big-O", "jaraco.functools", "jaraco.itertools", "more-itertools", "pytest (>=6)", "pytest-checkdocs (>=2.4)", "pytest-cov", "pytest-enabler (>=2.2)", "pytest-ignore-flaky", "pytest-mypy", "pytest-ruff (>=0.2.1)"] [extras] -api = ["Flask", "Flask-Cors", "Jinja2", "connexion", "pyopenssl"] +api = ["Flask", "Flask-Cors", "Jinja2", "connexion", "flask-opentracing", "jaeger-client", "pyopenssl"] aws = ["uWSGI"] [metadata] lock-version = "2.0" python-versions = ">=3.9.0,<3.11" -content-hash = "a5d0f2dd9e8e4346048dd8f2cd798a092d375714a5a3e1c7d86cfaf23d6e96fc" +content-hash = "5bf0c831977694ea541db24481181ec1980ec9589a2adbd9f30ed0fe7f2b2742" diff --git a/pyproject.toml b/pyproject.toml index 7c2bb991c..3c2795140 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -47,9 +47,9 @@ graphviz = "^0.20.0" inflection = "^0.5.1" jsonschema = "^4.0.0" networkx = ">=2.2.8" -numpy = "^1.21.1" +numpy = "^1.26.4" oauth2client = "^4.1.0" # Specified because of bug in version ^4.0.0 -pandas = "^2.0.0" +pandas = "^2.2.2" pygsheets = "^2.0.4" PyYAML = "^6.0.0" rdflib = "^6.0.0" @@ -67,16 +67,18 @@ dateparser = "^1.1.4" pandarallel = "^1.6.4" schematic-db = {version = "0.0.41", extras = ["synapse"]} pyopenssl = {version = "^23.0.0", optional = true} -typing-extensions = "<4.6.0" dataclasses-json = "^0.6.1" +pydantic = "^1.10.4" connexion = {extras = ["swagger-ui"], version = "^2.8.0", optional = true} Flask = {version = "2.1.3", optional = true} Flask-Cors = {version = "^3.0.10", optional = true} uWSGI = {version = "^2.0.21", optional = true} Jinja2 = {version = ">2.11.3", optional = true} +jaeger-client = {version = "^4.8.0", optional = true} +flask-opentracing = {version="^2.0.0", optional = true} [tool.poetry.extras] -api = ["connexion", "Flask", "Flask-Cors", "Jinja2", "pyopenssl"] +api = ["connexion", "Flask", "Flask-Cors", "Jinja2", "pyopenssl", "jaeger-client", "flask-opentracing"] aws = ["uWSGI"] diff --git a/schematic/configuration/configuration.py b/schematic/configuration/configuration.py index 1bd3f1c40..63bf55313 100644 --- a/schematic/configuration/configuration.py +++ b/schematic/configuration/configuration.py @@ -164,14 +164,6 @@ def model_location(self) -> str: """ return self._model_config.location - @property - def service_account_credentials_synapse_id(self) -> str: - """ - Returns: - str: The Synapse id of the Google service account credentials. - """ - return self._google_sheets_config.service_acct_creds_synapse_id - @property def service_account_credentials_path(self) -> str: """ diff --git a/schematic/configuration/dataclasses.py b/schematic/configuration/dataclasses.py index 7fbc7df57..4b3d1560f 100644 --- a/schematic/configuration/dataclasses.py +++ b/schematic/configuration/dataclasses.py @@ -124,12 +124,10 @@ class GoogleSheetsConfig: strict_validation: When doing google sheet validation (regex match) with the validation rules. True is alerting the user and not allowing entry of bad values. False is warning but allowing the entry on to the sheet. - service_acct_creds_synapse_id: The Synapse id of the Google service account credentials. service_acct_creds: Path to the Google service account credentials, either absolute or relative to this file """ - service_acct_creds_synapse_id: str = "syn25171627" service_acct_creds: str = "schematic_service_account_creds.json" strict_validation: bool = True @@ -151,7 +149,6 @@ def validate_string_is_not_empty(cls, value: str) -> str: raise ValueError(f"{value} is an empty string") return value - @validator("service_acct_creds_synapse_id") @classmethod def validate_synapse_id(cls, value: str) -> str: """Check if string is a valid synapse id diff --git a/schematic/manifest/generator.py b/schematic/manifest/generator.py index 5aced191e..d7eb16c30 100644 --- a/schematic/manifest/generator.py +++ b/schematic/manifest/generator.py @@ -32,8 +32,10 @@ from schematic.configuration.configuration import CONFIG from schematic.utils.google_api_utils import export_manifest_drive_service +from opentelemetry import trace logger = logging.getLogger(__name__) +tracer = trace.get_tracer("Schematic") class ManifestGenerator(object): @@ -1289,6 +1291,7 @@ def _gather_all_fields(self, fields, json_schema): ) return required_metadata_fields + @tracer.start_as_current_span("ManifestGenerator::get_empty_manifest") def get_empty_manifest( self, strict: Optional[bool], @@ -1334,6 +1337,7 @@ def _get_missing_columns(self, headers_1: list, headers_2: list) -> list: """ return set(headers_1) - set(headers_2) + @tracer.start_as_current_span("ManifestGenerator::set_dataframe_by_url") def set_dataframe_by_url( self, manifest_url: str, @@ -1425,6 +1429,7 @@ def map_annotation_names_to_display_names( # Use the above dictionary to rename columns in question return annotations.rename(columns=label_map) + @tracer.start_as_current_span("ManifestGenerator::get_manifest_with_annotations") def get_manifest_with_annotations( self, annotations: pd.DataFrame, strict: Optional[bool] = None ) -> Tuple[ps.Spreadsheet, pd.DataFrame]: @@ -1465,6 +1470,7 @@ def get_manifest_with_annotations( return manifest_url, manifest_df + @tracer.start_as_current_span("ManifestGenerator::export_sheet_to_excel") def export_sheet_to_excel( self, title: str = None, manifest_url: str = None, output_location: str = None ) -> str: @@ -1514,6 +1520,7 @@ def export_sheet_to_excel( return output_excel_file_path + @tracer.start_as_current_span("ManifestGenerator::_handle_output_format_logic") def _handle_output_format_logic( self, output_format: str = None, @@ -1570,6 +1577,7 @@ def _handle_output_format_logic( return dataframe @staticmethod + @tracer.start_as_current_span("ManifestGenerator::create_single_manifest") def create_single_manifest( path_to_data_model: str, graph_data_model: nx.MultiDiGraph, @@ -1623,6 +1631,7 @@ def create_single_manifest( return result @staticmethod + @tracer.start_as_current_span("ManifestGenerator::create_manifests") def create_manifests( path_to_data_model: str, data_types: list, @@ -1751,6 +1760,7 @@ def create_manifests( return all_results + @tracer.start_as_current_span("ManifestGenerator::get_manifest") def get_manifest( self, dataset_id: str = None, @@ -1998,6 +2008,9 @@ def _format_new_excel_column(self, worksheet, new_column_index: int, col: str): ) return worksheet + @tracer.start_as_current_span( + "ManifestGenerator::populate_existing_excel_spreadsheet" + ) def populate_existing_excel_spreadsheet( self, existing_excel_path: str = None, additional_df: pd.DataFrame = None ): diff --git a/schematic/models/metadata.py b/schematic/models/metadata.py index 4bb00e37b..2747f81d7 100644 --- a/schematic/models/metadata.py +++ b/schematic/models/metadata.py @@ -19,9 +19,12 @@ from schematic.utils.df_utils import load_df from schematic.models.validate_manifest import validate_all +from opentelemetry import trace logger = logging.getLogger(__name__) +tracer = trace.get_tracer("Schematic") + class MetadataModel(object): """Metadata model wrapper around schema.org specification graph. @@ -317,6 +320,7 @@ def populateModelManifest( manifestPath, emptyManifestURL, return_excel=return_excel, title=title ) + @tracer.start_as_current_span("MetadataModel::submit_metadata_manifest") def submit_metadata_manifest( # pylint: disable=too-many-arguments, too-many-locals self, manifest_path: str, diff --git a/schematic/schemas/commands.py b/schematic/schemas/commands.py index 17f622a6c..5b143f640 100644 --- a/schematic/schemas/commands.py +++ b/schematic/schemas/commands.py @@ -3,7 +3,7 @@ import logging import time import re -from typing import get_args +from typing import get_args, Optional, Any import click import click_log # type: ignore @@ -29,7 +29,7 @@ # invoke_without_command=True -> forces the application not to show aids before # losing them with a --h @click.group(context_settings=CONTEXT_SETTINGS, invoke_without_command=True) -def schema(): # use as `schematic model ...` +def schema() -> None: # use as `schematic model ...` """ Sub-commands for Schema related utilities/methods. """ @@ -59,7 +59,9 @@ def schema(): # use as `schematic model ...` metavar="", help=query_dict(schema_commands, ("schema", "convert", "output_jsonld")), ) -def convert(schema, data_model_labels, output_jsonld): +def convert( + schema: Any, data_model_labels: DisplayLabelType, output_jsonld: Optional[str] +) -> None: """ Running CLI to convert data model specification in CSV format to data model in JSON-LD format. diff --git a/schematic/schemas/data_model_graph.py b/schematic/schemas/data_model_graph.py index 515421491..4aae01a22 100644 --- a/schematic/schemas/data_model_graph.py +++ b/schematic/schemas/data_model_graph.py @@ -5,6 +5,7 @@ import networkx as nx # type: ignore import graphviz # type: ignore +from opentelemetry import trace from schematic.schemas.data_model_edges import DataModelEdges from schematic.schemas.data_model_nodes import DataModelNodes @@ -20,8 +21,11 @@ from schematic.utils.viz_utils import visualize from schematic.utils.validate_utils import rule_in_rule_list +logger = logging.getLogger(__name__) + logger = logging.getLogger(__name__) +tracer = trace.get_tracer("Schematic") class DataModelGraphMeta: # pylint: disable=too-few-public-methods @@ -29,13 +33,15 @@ class DataModelGraphMeta: # pylint: disable=too-few-public-methods _instances: dict = {} - def __call__(cls, *args: Any, **kwargs: Any): # pylint: disable=no-self-argument + def __call__( # pylint: disable=no-self-argument + cls, *args: Any, **kwargs: Any + ) -> Any: """ Possible changes to the value of the `__init__` argument do not affect the returned instance. """ if cls not in cls._instances: - instance = super().__call__(*args, **kwargs) # pylint: disable=no-member + instance = super().__call__(*args, **kwargs) # type: ignore # pylint: disable=no-member cls._instances[cls] = instance return cls._instances[cls] @@ -83,6 +89,7 @@ def __init__( ) self.graph = self.generate_data_model_graph() + @tracer.start_as_current_span("DataModelGraph::generate_data_model_graph") def generate_data_model_graph(self) -> nx.MultiDiGraph: """ Generate NetworkX Graph from the Relationships/attributes dictionary, the graph is built @@ -295,14 +302,14 @@ def get_component_node_validation_rules( manifest_component: str, node_label: Optional[str] = None, node_display_name: Optional[str] = None, - ) -> list[str]: + ) -> list: """Get valdation rules for a given node and component. Args: manifest_component: str, manifest component display name that the node belongs to. node_label: str, Label of the node you would want to get the comment for. node_display_name: str, node display name for the node being queried. Returns: - validation_rules: list[str], validation rules list for a given node and component. + validation_rules: list, validation rules list for a given node and component. """ # get any additional validation rules associated with this node (e.g. can this node # be mapped to a list of other nodes) @@ -312,11 +319,14 @@ def get_component_node_validation_rules( # Parse the validation rules per component if applicable if node_validation_rules and isinstance(node_validation_rules, dict): - node_validation_rules = extract_component_validation_rules( + node_validation_rules_list = extract_component_validation_rules( manifest_component=manifest_component, - validation_rules_dict=node_validation_rules, + validation_rules_dict=node_validation_rules, # type: ignore ) - return node_validation_rules + else: + assert isinstance(node_validation_rules, list) + node_validation_rules_list = node_validation_rules + return node_validation_rules_list def get_component_requirements( self, @@ -830,7 +840,9 @@ def find_child_classes(self, schema_class: str) -> list: Returns: list of children to the schema_class. """ - return unlist(list(self.graph.successors(schema_class))) + child_classes = unlist(list(self.graph.successors(schema_class))) + assert isinstance(child_classes, list) + return child_classes def find_class_specific_properties(self, schema_class: str) -> list[str]: """Find properties specifically associated with a given class diff --git a/schematic/schemas/data_model_json_schema.py b/schematic/schemas/data_model_json_schema.py index d21ca2744..cb58102c7 100644 --- a/schematic/schemas/data_model_json_schema.py +++ b/schematic/schemas/data_model_json_schema.py @@ -1,5 +1,6 @@ "Data Model Json Schema" +import json import logging import os from typing import Any, Optional @@ -9,6 +10,7 @@ from schematic.schemas.data_model_graph import DataModelGraphExplorer from schematic.schemas.data_model_relationships import DataModelRelationships from schematic.utils.validate_utils import rule_in_rule_list +from schematic.utils.schema_utils import get_json_schema_log_file_path logger = logging.getLogger(__name__) @@ -73,7 +75,7 @@ def get_non_blank_schema( return non_blank_schema def get_range_schema( - self, node_range: list[str], node_name: str, blank=False + self, node_range: list[str], node_name: str, blank: bool = False ) -> dict[str, dict[str, list[str]]]: """ Add a list of nodes to the "enum" key in a given JSON schema object. @@ -227,7 +229,7 @@ def get_json_validation_schema( # otherwise, by default allow any values schema_valid_vals = {node_display_name: {}} - json_schema["properties"].update(schema_valid_vals) + json_schema["properties"].update(schema_valid_vals) # type: ignore # set schema conditional dependencies for node in reverse_dependencies[node_display_name]: @@ -289,7 +291,7 @@ def get_json_validation_schema( } # update conditional-dependency rules in json schema - json_schema["allOf"].append( + json_schema["allOf"].append( # type: ignore schema_conditional_dependencies ) @@ -317,9 +319,9 @@ def get_json_validation_schema( node_name=node_display_name ) - json_schema["properties"].update(schema_valid_vals) + json_schema["properties"].update(schema_valid_vals) # type: ignore # add node to required fields - json_schema["required"] += [node_display_name] + json_schema["required"] += [node_display_name] # type: ignore elif process_node in root_dependencies: # node doesn't have conditionals and is not required; it belongs in the @@ -343,7 +345,7 @@ def get_json_validation_schema( else: schema_valid_vals = {node_display_name: {}} - json_schema["properties"].update(schema_valid_vals) + json_schema["properties"].update(schema_valid_vals) # type: ignore else: # node doesn't have conditionals and it is not required and it @@ -391,9 +393,18 @@ def get_json_validation_schema( # If no config value and SchemaGenerator was initialized with # a JSON-LD path, construct if self.jsonld_path is not None: - self.jsonld_path_root, _ = os.path.splitext(self.jsonld_path) - prefix = self.jsonld_path_root - prefix_root, prefix_ext = os.path.splitext(prefix) - if prefix_ext == ".model": - prefix = prefix_root - return json_schema + json_schema_log_file_path = get_json_schema_log_file_path( + data_model_path=self.jsonld_path, source_node=source_node + ) + if json_schema_log_file_path is None: + logger.info( + "The JSON schema file can be inspected by setting the following " + "nested key in the configuration: (model > location)." + ) + else: + json_schema_dirname = os.path.dirname(json_schema_log_file_path) + if json_schema_dirname != "": + os.makedirs(json_schema_dirname, exist_ok=True) + with open(json_schema_log_file_path, "w", encoding="UTF-8") as js_f: + json.dump(json_schema, js_f, indent=2) + return json_schema # type: ignore diff --git a/schematic/schemas/data_model_jsonld.py b/schematic/schemas/data_model_jsonld.py index 58f86cfe6..0a2464ecb 100644 --- a/schematic/schemas/data_model_jsonld.py +++ b/schematic/schemas/data_model_jsonld.py @@ -3,10 +3,12 @@ import json import logging import copy +from typing import Union + from dataclasses import dataclass, field from dataclasses_json import config, dataclass_json -import networkx as nx +import networkx as nx # type: ignore from schematic.schemas.data_model_graph import DataModelGraphExplorer from schematic.schemas.data_model_relationships import DataModelRelationships @@ -125,17 +127,17 @@ def __init__(self, graph: nx.MultiDiGraph, output_path: str = ""): # Gather the templates base_template = BaseTemplate() self.base_jsonld_template = json.loads( - base_template.to_json() # pylint:disable=no-member + base_template.to_json() # type: ignore # pylint:disable=no-member ) property_template = PropertyTemplate() self.property_template = json.loads( - property_template.to_json() # pylint:disable=no-member + property_template.to_json() # type: ignore # pylint:disable=no-member ) class_template = ClassTemplate() self.class_template = json.loads( - class_template.to_json() # pylint:disable=no-member + class_template.to_json() # type: ignore # pylint:disable=no-member ) def get_edges_associated_with_node( @@ -177,9 +179,9 @@ def get_edges_associated_with_property_nodes( node_edges.append((node, node_2, edge_dict[edge_key])) return node_edges - def add_edge_rels_to_template( + def add_edge_rels_to_template( # pylint:disable=too-many-branches self, template: dict, rel_vals: dict, node: str - ): # pylint:disable=too-many-branches + ) -> dict: """ Args: template, dict: single class or property JSONLD template that is in the process of being @@ -271,7 +273,9 @@ def add_edge_rels_to_template( ) return template - def add_node_info_to_template(self, template, rel_vals, node): + def add_node_info_to_template( + self, template: dict, rel_vals: dict, node: str + ) -> dict: """For a given node and relationship, add relevant value to template Args: template, dict: single class or property JSONLD template that is in the process @@ -473,7 +477,9 @@ def reorder_template_entries(self, template: dict) -> dict: ) edge_weights_dict = {edge: i for i, edge in enumerate(sorted_edges)} - ordered_edges = [0] * len(edge_weights_dict.keys()) + ordered_edges: list[Union[int, dict]] = [0] * len( + edge_weights_dict.keys() + ) for edge, normalized_weight in edge_weights_dict.items(): ordered_edges[normalized_weight] = {"@id": "bts:" + edge} @@ -488,7 +494,7 @@ def reorder_template_entries(self, template: dict) -> dict: template[jsonld_key] = ordered_edges return template - def generate_jsonld_object(self): + def generate_jsonld_object(self) -> dict: """Create the JSONLD object. Returns: jsonld_object, dict: JSONLD object containing all nodes and related information @@ -513,7 +519,7 @@ def generate_jsonld_object(self): return json_ld_template -def convert_graph_to_jsonld(graph): +def convert_graph_to_jsonld(graph: nx.MultiDiGraph) -> dict: """convert graph to jsonld""" # Make the JSONLD object data_model_jsonld_converter = DataModelJsonLD(graph=graph) diff --git a/schematic/schemas/data_model_nodes.py b/schematic/schemas/data_model_nodes.py index 24de9cf37..a8ea4fd09 100644 --- a/schematic/schemas/data_model_nodes.py +++ b/schematic/schemas/data_model_nodes.py @@ -1,6 +1,6 @@ """Data model Nodes""" -from typing import Optional, Callable +from typing import Optional, Callable, Any from inspect import isfunction import networkx as nx # type: ignore @@ -14,13 +14,14 @@ convert_bool_to_str, parse_validation_rules, DisplayLabelType, + EntryType, ) class DataModelNodes: """Data model Nodes""" - def __init__(self, attribute_relationships_dict): + def __init__(self, attribute_relationships_dict: dict): self.namespaces = { "rdf": Namespace("http://www.w3.org/1999/02/22-rdf-syntax-ns#") } @@ -123,15 +124,17 @@ def get_data_model_properties(self, attr_rel_dict: dict) -> list: properties = list(set(properties)) return properties - def get_entry_type(self, node_display_name: str) -> str: + def get_entry_type(self, node_display_name: str) -> EntryType: """Get the entry type of the node, property or class. + Args: - node_display_name, str: display name of target node. + node_display_name (str): display name of target node. + Returns: - entry_type, str: returns 'property' or 'class' based on data model specifications. + EntryType: returns 'property' or 'class' based on data model specifications. """ if node_display_name in self.properties: - entry_type = "property" + entry_type: EntryType = "property" else: entry_type = "class" return entry_type @@ -141,11 +144,11 @@ def run_rel_functions( rel_func: Callable, node_display_name: str = "", key: str = "", - attr_relationships=None, - csv_header="", - entry_type="", + attr_relationships: Optional[dict] = None, + csv_header: str = "", + entry_type: EntryType = "class", data_model_labels: DisplayLabelType = "class_label", - ): + ) -> Any: """ This function exists to centralzie handling of functions for filling out node information, makes sure all the proper parameters are passed to each function. @@ -259,7 +262,9 @@ def generate_node_dict( # Look through relationship types that represent values (i.e. do not define edges) for key, csv_header in self.value_relationships.items(): # Get key and defalt values current relationship type. - rel_key, rel_node_dict = self.get_rel_node_dict_info(key) + rel_node = self.get_rel_node_dict_info(key) + assert rel_node is not None + rel_key, rel_node_dict = rel_node # If we have information to add about this particular node, get it if csv_header in attr_relationships.keys(): @@ -322,6 +327,6 @@ def generate_node(self, graph: nx.MultiDiGraph, node_dict: dict) -> nx.MultiDiGr graph.add_node(node_dict["label"], **node_dict) return graph - def edit_node(self): + def edit_node(self) -> None: """Stub for future node editor.""" return diff --git a/schematic/schemas/data_model_parser.py b/schematic/schemas/data_model_parser.py index 2ddda42bd..0da26e933 100644 --- a/schematic/schemas/data_model_parser.py +++ b/schematic/schemas/data_model_parser.py @@ -5,6 +5,7 @@ import logging import pandas as pd +from opentelemetry import trace from schematic.utils.df_utils import load_df from schematic.utils.io_utils import load_json @@ -14,7 +15,9 @@ from schematic import LOADER -logger = logging.getLogger("Synapse storage") +logger = logging.getLogger("Schemas") + +tracer = trace.get_tracer("Schematic") class DataModelParser: @@ -84,6 +87,7 @@ def parse_base_model(self) -> dict: base_model = jsonld_parser.parse_jsonld_model(base_model_path) return base_model + @tracer.start_as_current_span("DataModelParser::parse_model") def parse_model(self) -> dict[str, dict[str, Any]]: """Given a data model type, instantiate and call the appropriate data model parser. Returns: @@ -119,7 +123,7 @@ def parse_model(self) -> dict[str, dict[str, Any]]: class DataModelCSVParser: """DataModelCSVParser""" - def __init__(self): + def __init__(self) -> None: # Instantiate DataModelRelationships self.dmr = DataModelRelationships() # Load relationships dictionary. @@ -230,10 +234,11 @@ def gather_csv_attributes_relationships( ) return attr_rel_dictionary + @tracer.start_as_current_span("Schemas::DataModelCSVParser::parse_csv_model") def parse_csv_model( self, path_to_data_model: str, - ): + ) -> dict[str, dict[str, Any]]: """Load csv data model and parse into an attributes:relationships dictionary Args: path_to_data_model, str: path to data model @@ -256,7 +261,7 @@ class DataModelJSONLDParser: def __init__( self, - ): + ) -> None: # Instantiate DataModelRelationships self.dmr = DataModelRelationships() # Load relationships dictionary. @@ -283,7 +288,7 @@ def parse_jsonld_dicts( # Retrieve ID from a dictionary recording the ID if set(rel_entry.keys()) == {"@id"}: - parsed_rel_entry = rel_entry["@id"] + parsed_rel_entry: Union[str, dict[str, str]] = rel_entry["@id"] # Parse any remaining dictionaries else: parsed_rel_entry = rel_entry @@ -309,7 +314,7 @@ def parse_entry( """ # Parse dictionary entries if isinstance(rel_entry, dict): - parsed_rel_entry = self.parse_jsonld_dicts(rel_entry) + parsed_rel_entry: Any = self.parse_jsonld_dicts(rel_entry) # Parse list of dictionaries to make a list of entries with context stripped (will update # this section when contexts added.) @@ -338,7 +343,7 @@ def parse_entry( return parsed_rel_entry - def label_to_dn_dict(self, model_jsonld: list[dict]): + def label_to_dn_dict(self, model_jsonld: list[dict]) -> dict: """ Generate a dictionary of labels to display name, so can easily look up display names using the label. @@ -358,7 +363,7 @@ def label_to_dn_dict(self, model_jsonld: list[dict]): def convert_entry_to_dn_label( self, parsed_rel_entry: Union[str, list], model_jsonld: list[dict] - ) -> Union[str, list]: + ) -> Union[str, list, None]: """Convert a parsed entry to display name, taking into account the entry type Args: parsed_rel_entry: an entry that has been parsed base on its input type @@ -372,15 +377,17 @@ def convert_entry_to_dn_label( dn_label_dict = self.label_to_dn_dict(model_jsonld=model_jsonld) # Handle if using the display name as the label if isinstance(parsed_rel_entry, list): - parsed_rel_entry = [ + dn_label: Union[str, list, None] = [ dn_label_dict.get(entry) if dn_label_dict.get(entry) else entry for entry in parsed_rel_entry ] elif isinstance(parsed_rel_entry, str): converted_label = dn_label_dict.get(parsed_rel_entry) if converted_label: - parsed_rel_entry = dn_label_dict.get(parsed_rel_entry) - return parsed_rel_entry + dn_label = dn_label_dict.get(parsed_rel_entry) + else: + dn_label = parsed_rel_entry + return dn_label def gather_jsonld_attributes_relationships(self, model_jsonld: list[dict]) -> dict: """ @@ -460,7 +467,7 @@ def gather_jsonld_attributes_relationships(self, model_jsonld: list[dict]) -> di for parsed_val in parsed_rel_entry: attr_in_dict = False # Get propert/parent key (displayName) - p_attr_key = "" + p_attr_key: Any = "" # Check if the parsed value is already a part of the # attr_rel_dictionary for attr_dn in attr_rel_dictionary: @@ -527,10 +534,11 @@ def gather_jsonld_attributes_relationships(self, model_jsonld: list[dict]) -> di ) return attr_rel_dictionary + @tracer.start_as_current_span("Schemas::DataModelJSONLDParser::parse_jsonld_model") def parse_jsonld_model( self, path_to_data_model: str, - ): + ) -> dict: """Convert raw JSONLD data model to attributes relationship dictionary. Args: path_to_data_model: str, path to JSONLD data model diff --git a/schematic/schemas/data_model_relationships.py b/schematic/schemas/data_model_relationships.py index f83de5d8e..c222285da 100644 --- a/schematic/schemas/data_model_relationships.py +++ b/schematic/schemas/data_model_relationships.py @@ -192,7 +192,7 @@ def define_data_model_relationships(self) -> dict: return map_data_model_relationships - def define_required_csv_headers(self): + def define_required_csv_headers(self) -> list: """ Helper function to retrieve required CSV headers, alert if required header was not provided. diff --git a/schematic/schemas/data_model_validator.py b/schematic/schemas/data_model_validator.py index 897c33738..ca3b7e31b 100644 --- a/schematic/schemas/data_model_validator.py +++ b/schematic/schemas/data_model_validator.py @@ -85,7 +85,7 @@ def check_graph_has_required_node_fields(self) -> list[str]: ) return error - def run_cycles(self): + def run_cycles(self) -> None: """run_cycles""" cycles = nx.simple_cycles(self.graph) if cycles: # pylint:disable=using-constant-test @@ -188,27 +188,27 @@ def check_reserved_names(self) -> list[str]: ) return error - def check_namespace_overlap(self): + def check_namespace_overlap(self) -> list: """ Check if name is repeated. Implement in the future """ - warning = [] + warning: list = [] return warning - def check_for_orphan_attributes(self): + def check_for_orphan_attributes(self) -> list: """ Check if attribute is specified but not connected to another attribute or component. Implement in future """ - warning = [] + warning: list = [] return warning - def check_namespace_similarity(self): + def check_namespace_similarity(self) -> list: """ Using AI, check if submitted attributes or valid values are similar to other ones, warn users. Implement in future """ - warning = [] + warning: list = [] return warning diff --git a/schematic/schemas/json_schema_validator.py b/schematic/schemas/json_schema_validator.py index 7369c1f45..0a1760c79 100644 --- a/schematic/schemas/json_schema_validator.py +++ b/schematic/schemas/json_schema_validator.py @@ -1,6 +1,8 @@ """Json Schema Validator""" import os +from typing import Any + from jsonschema import validate from schematic.utils.io_utils import load_schemaorg, load_json @@ -46,12 +48,13 @@ class SchemaValidator: """ - def __init__(self, schema): + def __init__(self, schema: Any) -> None: self.schemaorg = {"schema": load_schemaorg(), "classes": [], "properties": []} for _schema in self.schemaorg["schema"]["@graph"]: for _record in _schema["@graph"]: if "@type" in _record: _type = str2list(_record["@type"]) + assert isinstance(_type, list) if "rdfs:Property" in _type: self.schemaorg["properties"].append(_record["@id"]) elif "rdfs:Class" in _type: @@ -61,70 +64,74 @@ def __init__(self, schema): "classes": [], "properties": [], } - for _record in self.extension_schema["schema"]["@graph"]: + for _record in self.extension_schema["schema"]["@graph"]: # type: ignore _type = str2list(_record["@type"]) + assert isinstance(_type, list) if "rdfs:Property" in _type: - self.extension_schema["properties"].append(_record["@id"]) + self.extension_schema["properties"].append(_record["@id"]) # type: ignore elif "rdfs:Class" in _type: - self.extension_schema["classes"].append(_record["@id"]) + self.extension_schema["classes"].append(_record["@id"]) # type: ignore self.all_classes = self.schemaorg["classes"] + self.extension_schema["classes"] - def validate_class_label(self, label_uri): + def validate_class_label(self, label_uri: str) -> None: """Check if the first character of class label is capitalized""" label = extract_name_from_uri_or_curie(label_uri) assert label[0].isupper() - def validate_property_label(self, label_uri): + def validate_property_label(self, label_uri: str) -> None: """Check if the first character of property label is lower case""" label = extract_name_from_uri_or_curie(label_uri) assert label[0].islower() - def validate_subclassof_field(self, subclassof_value): + def validate_subclassof_field(self, subclassof_value: dict) -> None: """Check if the value of "subclassof" is included in the schema file""" - subclassof_value = dict2list(subclassof_value) + subclassof_value_list = dict2list(subclassof_value) + assert isinstance(subclassof_value_list, list) for record in subclassof_value: assert record["@id"] in self.all_classes - def validate_domain_includes_field(self, domainincludes_value): + def validate_domain_includes_field(self, domainincludes_value: dict) -> None: """Check if the value of "domainincludes" is included in the schema file """ - domainincludes_value = dict2list(domainincludes_value) - for record in domainincludes_value: + domainincludes_value_list = dict2list(domainincludes_value) + assert isinstance(domainincludes_value_list, list) + for record in domainincludes_value_list: assert ( record["@id"] in self.all_classes ), f"value of domainincludes not recorded in schema: {domainincludes_value}" - def validate_range_includes_field(self, rangeincludes_value): + def validate_range_includes_field(self, rangeincludes_value: dict) -> None: """Check if the value of "rangeincludes" is included in the schema file """ - rangeincludes_value = dict2list(rangeincludes_value) - for record in rangeincludes_value: + rangeincludes_value_list = dict2list(rangeincludes_value) + assert isinstance(rangeincludes_value_list, list) + for record in rangeincludes_value_list: assert record["@id"] in self.all_classes - def check_whether_atid_and_label_match(self, record): + def check_whether_atid_and_label_match(self, record: dict) -> None: """Check if @id field matches with the "rdfs:label" field""" _id = extract_name_from_uri_or_curie(record["@id"]) assert _id == record["rdfs:label"], f"id and label not match: {record}" - def check_duplicate_labels(self): + def check_duplicate_labels(self) -> None: """Check for duplication in the schema""" labels = [ _record["rdfs:label"] - for _record in self.extension_schema["schema"]["@graph"] + for _record in self.extension_schema["schema"]["@graph"] # type: ignore ] duplicates = find_duplicates(labels) if len(duplicates) == 0: raise ValueError("Duplicates detected in graph: ", duplicates) - def validate_schema(self, schema): + def validate_schema(self, schema: Any) -> None: """Validate schema against SchemaORG standard""" json_schema_path = os.path.join("validation_schemas", "schema.json") json_schema = load_json(json_schema_path) return validate(schema, json_schema) - def validate_property_schema(self, schema): + def validate_property_schema(self, schema: Any) -> None: """Validate schema against SchemaORG property definition standard""" json_schema_path = os.path.join( "validation_schemas", "property_json_schema.json" @@ -132,16 +139,16 @@ def validate_property_schema(self, schema): json_schema = load_json(json_schema_path) return validate(schema, json_schema) - def validate_class_schema(self, schema): + def validate_class_schema(self, schema: Any) -> None: """Validate schema against SchemaORG class definition standard""" json_schema_path = os.path.join("validation_schemas", "class_json_schema.json") json_schema = load_json(json_schema_path) return validate(schema, json_schema) - def validate_full_schema(self): + def validate_full_schema(self) -> None: """validate full schema""" self.check_duplicate_labels() - for record in self.extension_schema["schema"]["@graph"]: + for record in self.extension_schema["schema"]["@graph"]: # type: ignore self.check_whether_atid_and_label_match(record) if record["@type"] == "rdf:Class": self.validate_class_schema(record) diff --git a/schematic/store/synapse.py b/schematic/store/synapse.py index a15137ae8..688bbce4f 100644 --- a/schematic/store/synapse.py +++ b/schematic/store/synapse.py @@ -68,9 +68,12 @@ from schematic.store.base import BaseStorage from schematic.exceptions import AccessCredentialsError from schematic.configuration.configuration import CONFIG +from opentelemetry import trace logger = logging.getLogger("Synapse storage") +tracer = trace.get_tracer("Schematic") + @dataclass class ManifestDownload(object): @@ -248,6 +251,7 @@ def _purge_synapse_cache( # instead of guessing how much space that we left, print out .synapseCache here logger.info(f"the total size of .synapseCache is: {nbytes} bytes") + @tracer.start_as_current_span("SynapseStorage::_query_fileview") def _query_fileview(self): self._purge_synapse_cache() try: @@ -412,6 +416,7 @@ def getStorageProjects(self, project_scope: List = None) -> list[tuple[str, str] return sorted_projects_list + @tracer.start_as_current_span("SynapseStorage::getStorageDatasetsInProject") def getStorageDatasetsInProject(self, projectId: str) -> list[tuple[str, str]]: """Gets all datasets in folder under a given storage project that the current user has access to. @@ -456,6 +461,7 @@ def getStorageDatasetsInProject(self, projectId: str) -> list[tuple[str, str]]: return sorted_dataset_list + @tracer.start_as_current_span("SynapseStorage::getFilesInStorageDataset") def getFilesInStorageDataset( self, datasetId: str, fileNames: List = None, fullpath: bool = True ) -> List[Tuple[str, str]]: @@ -525,6 +531,7 @@ def _get_manifest_id(self, manifest: pd.DataFrame) -> str: return manifest_syn_id + @tracer.start_as_current_span("SynapseStorage::getDatasetManifest") def getDatasetManifest( self, datasetId: str, @@ -712,6 +719,7 @@ def fill_in_entity_id_filename( manifest = manifest.fillna("") return dataset_files, manifest + @tracer.start_as_current_span("SynapseStorage::updateDatasetManifestFiles") def updateDatasetManifestFiles( self, dmge: DataModelGraphExplorer, datasetId: str, store: bool = True ) -> Union[Tuple[str, pd.DataFrame], None]: @@ -738,22 +746,26 @@ def updateDatasetManifestFiles( manifest_filepath = self.syn.get(manifest_id).path manifest = load_df(manifest_filepath) + manifest_is_file_based = "Filename" in manifest.columns - # update manifest with additional filenames, if any - # note that if there is an existing manifest and there are files in the dataset - # the columns Filename and entityId are assumed to be present in manifest schema - # TODO: use idiomatic panda syntax - - dataset_files, manifest = self.fill_in_entity_id_filename(datasetId, manifest) - if dataset_files: - # update the manifest file, so that it contains the relevant entity IDs - if store: - manifest.to_csv(manifest_filepath, index=False) + if manifest_is_file_based: + # update manifest with additional filenames, if any + # note that if there is an existing manifest and there are files in the dataset + # the columns Filename and entityId are assumed to be present in manifest schema + # TODO: use idiomatic panda syntax - # store manifest and update associated metadata with manifest on Synapse - manifest_id = self.associateMetadataWithFiles( - dmge, manifest_filepath, datasetId - ) + dataset_files, manifest = self.fill_in_entity_id_filename( + datasetId, manifest + ) + if dataset_files: + # update the manifest file, so that it contains the relevant entity IDs + if store: + manifest.to_csv(manifest_filepath, index=False) + + # store manifest and update associated metadata with manifest on Synapse + manifest_id = self.associateMetadataWithFiles( + dmge, manifest_filepath, datasetId + ) return manifest_id, manifest @@ -794,6 +806,7 @@ def _get_file_entityIds( return files + @tracer.start_as_current_span("SynapseStorage::getProjectManifests") def getProjectManifests( self, projectId: str ) -> list[tuple[tuple[str, str], tuple[str, str], tuple[str, str]]]: @@ -1100,6 +1113,7 @@ def get_table_info(self, datasetId: str = None, projectId: str = None) -> List[s return {None: None} @missing_entity_handler + @tracer.start_as_current_span("SynapseStorage::uploadDB") def uploadDB( self, dmge: DataModelGraphExplorer, @@ -1147,6 +1161,7 @@ def uploadDB( return manifest_table_id, manifest, table_manifest + @tracer.start_as_current_span("SynapseStorage::formatDB") def formatDB(self, dmge, manifest, table_column_names): """ Method to format a manifest appropriatly for upload as table @@ -1209,6 +1224,7 @@ def formatDB(self, dmge, manifest, table_column_names): return col_schema, table_manifest + @tracer.start_as_current_span("SynapseStorage::buildDB") def buildDB( self, datasetId: str, @@ -1284,6 +1300,7 @@ def buildDB( return manifest_table_id + @tracer.start_as_current_span("SynapseStorage::upload_manifest_file") def upload_manifest_file( self, manifest, @@ -1330,7 +1347,10 @@ def upload_manifest_file( ).id synapseutils.copy_functions.changeFileMetaData( - syn=self.syn, entity=manifest_synapse_file_id, downloadAs=file_name_new + syn=self.syn, + entity=manifest_synapse_file_id, + downloadAs=file_name_new, + forceVersion=False, ) return manifest_synapse_file_id @@ -1395,6 +1415,7 @@ def format_row_annotations( return annos @missing_entity_handler + @tracer.start_as_current_span("SynapseStorage::format_manifest_annotations") def format_manifest_annotations(self, manifest, manifest_synapse_id): """ Set annotations for the manifest (as a whole) so they can be applied to the manifest table or csv. @@ -1604,6 +1625,7 @@ def _generate_table_name(self, manifest): table_name = "synapse_storage_manifest_table" return table_name, component_name + @tracer.start_as_current_span("SynapseStorage::_add_annotations") def _add_annotations( self, dmge, @@ -1653,6 +1675,7 @@ def _create_entity_id(self, idx, row, manifest, datasetId): manifest.loc[idx, "entityId"] = entityId return manifest, entityId + @tracer.start_as_current_span("SynapseStorage::add_annotations_to_entities_files") def add_annotations_to_entities_files( self, dmge, @@ -1717,6 +1740,7 @@ def add_annotations_to_entities_files( logger.info(f"Added annotations to entity: {entityId}") return manifest + @tracer.start_as_current_span("SynapseStorage::upload_manifest_as_table") def upload_manifest_as_table( self, dmge: DataModelGraphExplorer, @@ -1810,6 +1834,7 @@ def upload_manifest_as_table( self.syn.set_annotations(manifest_annotations) return manifest_synapse_file_id + @tracer.start_as_current_span("SynapseStorage::upload_manifest_as_csv") def upload_manifest_as_csv( self, dmge, @@ -1868,6 +1893,7 @@ def upload_manifest_as_csv( return manifest_synapse_file_id + @tracer.start_as_current_span("SynapseStorage::upload_manifest_combo") def upload_manifest_combo( self, dmge, @@ -1957,6 +1983,7 @@ def upload_manifest_combo( self.syn.set_annotations(manifest_annotations) return manifest_synapse_file_id + @tracer.start_as_current_span("SynapseStorage::associateMetadataWithFiles") def associateMetadataWithFiles( self, dmge: DataModelGraphExplorer, diff --git a/schematic/utils/google_api_utils.py b/schematic/utils/google_api_utils.py index 9a5d870ca..b705e0419 100644 --- a/schematic/utils/google_api_utils.py +++ b/schematic/utils/google_api_utils.py @@ -11,7 +11,6 @@ from googleapiclient.discovery import build, Resource # type: ignore from google.oauth2 import service_account # type: ignore from schematic.configuration.configuration import CONFIG -from schematic.store.synapse import SynapseStorage logger = logging.getLogger(__name__) @@ -67,39 +66,6 @@ def build_service_account_creds() -> GoogleServiceAcountCreds: return creds -def download_creds_file() -> None: - """Download google credentials file""" - syn = SynapseStorage.login() - - # if file path of service_account does not exist - # and if an environment variable related to service account is not found - # regenerate service_account credentials - if ( - not os.path.exists(CONFIG.service_account_credentials_path) - and "SERVICE_ACCOUNT_CREDS" not in os.environ - ): - # synapse ID of the 'schematic_service_account_creds.json' file - api_creds = CONFIG.service_account_credentials_synapse_id - - # Download in parent directory of SERVICE_ACCT_CREDS to - # ensure same file system for os.rename() - creds_dir = os.path.dirname(CONFIG.service_account_credentials_path) - - creds_file = syn.get(api_creds, downloadLocation=creds_dir) - os.rename(creds_file.path, CONFIG.service_account_credentials_path) - - logger.info( - "The credentials file has been downloaded " - f"to '{CONFIG.service_account_credentials_path}'" - ) - - elif "SERVICE_ACCOUNT_CREDS" in os.environ: - # remind users that "SERVICE_ACCOUNT_CREDS" as an environment variable is being used - logger.info( - "Using environment variable SERVICE_ACCOUNT_CREDS as the credential file." - ) - - @no_type_check def execute_google_api_requests(service, requests_body, **kwargs) -> Any: """ diff --git a/schematic/utils/schema_utils.py b/schematic/utils/schema_utils.py index a4565d420..bbf34940f 100644 --- a/schematic/utils/schema_utils.py +++ b/schematic/utils/schema_utils.py @@ -4,6 +4,7 @@ import json import logging +import os import string from typing import Literal, Union, Optional @@ -482,3 +483,20 @@ def strip_context(context_value: str) -> tuple[str, str]: elif "@" in context_value: context, value = context_value.split("@") return context, value + + +def get_json_schema_log_file_path(data_model_path: str, source_node: str) -> str: + """Get json schema log file name from the data_mdoel_path + Args: + data_model_path: str, path to the data model + source_node: str, root node to create the JSON schema for + Returns: + json_schema_log_file_path: str, file name for the log file + """ + data_model_path_root, _ = os.path.splitext(data_model_path) + prefix = data_model_path_root + prefix_root, prefix_ext = os.path.splitext(prefix) + if prefix_ext == ".model": + prefix = prefix_root + json_schema_log_file_path = f"{prefix}.{source_node}.schema.json" + return json_schema_log_file_path diff --git a/schematic_api/Dockerfile b/schematic_api/Dockerfile index 53f63533f..15e979dee 100644 --- a/schematic_api/Dockerfile +++ b/schematic_api/Dockerfile @@ -1,120 +1,126 @@ -FROM tiangolo/uwsgi-nginx-flask:python3.10 - -# add version tag as a build argument -ARG TAG - -# the environment variables defined here are the default -# and can be overwritten by docker run -e VARIABLE = XX -# or can be overwritten by .env when using docker compose -ENV PYTHONFAULTHANDLER=1 \ - PYTHONUNBUFFERED=1 \ - PYTHONHASHSEED=random \ - PIP_NO_CACHE_DIR=off \ - PIP_DISABLE_PIP_VERSION_CHECK=on \ - PIP_DEFAULT_TIMEOUT=200 \ - POETRY_VERSION=1.3.0 \ - APP_PARENT_DIR=/app \ - NGINX_CONFIG=/etc/nginx/conf.d \ - APP_DIR=/app/app \ - ROOT=/ \ - UWSGI_INI=/app/uwsgi.ini \ - NGINX_WORKER_PROCESSES=1 \ - VERSION=$TAG - -# Note: -# The starting number of uWSGI processes is controlled by the variable UWSGI_CHEAPER, by default set to 2. -# The maximum number of uWSGI processes is controlled by the variable UWSGI_PROCESSES, by default set to 16 -# By default, the image starts with 2 uWSGI processes running. When the server is experiencing a high load, it creates up to 16 uWSGI processes to handle it on demand. -# NGINX_MAX_UPLOAD is set to 0 by default that allows unlimited upload file sizes -# NGINX_WORKER_CONNECTIONS is set to 1024 by default that allows a maximum limit of 1024 connections per worker. -# NGINX_WORKER_OPEN_FILES is set to 2048 by default that allows 2048 open files - -# run open ssl and generate certificate -RUN apt update && \ - apt-get install openssl && \ - openssl req -x509 -nodes -days 365 \ - -subj "/C=CA/ST=QC/O=Company" \ - -newkey rsa:2048 -keyout /etc/ssl/private/localhost.key \ - -out /etc/ssl/certs/localhost.crt; - -# add dhparam.pem -# this step takes quite some time -RUN openssl dhparam -out /etc/ssl/dhparam.pem 4096 - -# copy config files that handle encryption to docker -WORKDIR ${NGINX_CONFIG} -COPY ./self-signed.conf ./ssl-params.conf ./certificate.conf ./ - - -# use custom uwsgi-nginx-entrypoint.sh -# this uwsgi-nginx-entrypoint.sh file is derived from: https://github.com/tiangolo/uwsgi-nginx-flask-docker/blob/master/docker-images/entrypoint.sh -# we have to modify it so that we could generate a different /etc/nginx/conf.d/nginx.conf file -WORKDIR ${ROOT} -COPY ./uwsgi-nginx-entrypoint.sh ./entrypoint2.sh -COPY ./uwsgi-nginx-entrypoint.sh ./uwsgi-nginx-entrypoint2.sh -RUN chmod +x uwsgi-nginx-entrypoint2.sh -RUN chmod +x entrypoint2.sh -RUN chown -R nginx /uwsgi-nginx-entrypoint2.sh -RUN chown -R nginx /entrypoint2.sh - -# install poetry -RUN pip install --no-cache-dir "poetry==$POETRY_VERSION" - -# set work directory -WORKDIR ${APP_PARENT_DIR} -RUN chown www-data:www-data ${APP_PARENT_DIR} - -# remove the old uwsgi.ini and main.py from the original image -RUN rm -rf ${APP_PARENT_DIR}/main.py -RUN rm -rf ${APP_PARENT_DIR}/uwsgi.ini - -# copy to use custom uwsgi.ini -COPY ./uwsgi.ini ./ - -# create a separate folder called app -RUN mkdir app -WORKDIR ${APP_DIR} - -# copy other files to app/app -# Note: run_api.py is not needed - -COPY ./pyproject.toml ./poetry.lock ./main.py ./ -COPY ./config_example.yml ./config.yml -RUN poetry config virtualenvs.create false -RUN poetry install --no-interaction --all-extras --no-root - -# copy schematic_api folder -COPY schematic_api ./schematic_api - -# copy great_expectations folder -COPY great_expectations ./great_expectations - -# copy tests folder because some endpoints by default download to the tests folder -COPY tests ./tests - -# change permission -RUN chown -R www-data:www-data ${APP_DIR} - -# allow downloading to synapse cache -RUN chown -R www-data:www-data /root - -# copy schematic -COPY schematic ./schematic - -# change permission -WORKDIR /var/www/ -#The -R option: make the command recursive, so it will change the owner of all files and subdirectories within a given folder. -RUN chown -R www-data:www-data /var/www/ - -RUN chown -R www-data:www-data /var/tmp/ - -# change work directory back -WORKDIR ${APP_DIR} - -# specify entrypoint again to generate config -# have to respecify CMD too -ENTRYPOINT ["/entrypoint2.sh"] -CMD ["/start.sh"] - -# Expose ports -EXPOSE 443 +FROM tiangolo/uwsgi-nginx-flask:python3.10 + +# add version tag as a build argument +ARG TAG + +# the environment variables defined here are the default +# and can be overwritten by docker run -e VARIABLE = XX +# or can be overwritten by .env when using docker compose +ENV PYTHONFAULTHANDLER=1 \ + PYTHONUNBUFFERED=1 \ + PYTHONHASHSEED=random \ + PIP_NO_CACHE_DIR=off \ + PIP_DISABLE_PIP_VERSION_CHECK=on \ + PIP_DEFAULT_TIMEOUT=200 \ + POETRY_VERSION=1.3.0 \ + APP_PARENT_DIR=/app \ + NGINX_CONFIG=/etc/nginx/conf.d \ + APP_DIR=/app/app \ + ROOT=/ \ + UWSGI_INI=/app/uwsgi.ini \ + NGINX_WORKER_PROCESSES=1 \ + VERSION=$TAG + + + +LABEL maintainer="Lingling Peng Andrew Lamb Gianna Jordan " +LABEL version=$TAG + + +# Note: +# The starting number of uWSGI processes is controlled by the variable UWSGI_CHEAPER, by default set to 2. +# The maximum number of uWSGI processes is controlled by the variable UWSGI_PROCESSES, by default set to 16 +# By default, the image starts with 2 uWSGI processes running. When the server is experiencing a high load, it creates up to 16 uWSGI processes to handle it on demand. +# NGINX_MAX_UPLOAD is set to 0 by default that allows unlimited upload file sizes +# NGINX_WORKER_CONNECTIONS is set to 1024 by default that allows a maximum limit of 1024 connections per worker. +# NGINX_WORKER_OPEN_FILES is set to 2048 by default that allows 2048 open files + +# run open ssl and generate certificate +RUN apt update && \ + apt-get install openssl && \ + openssl req -x509 -nodes -days 365 \ + -subj "/C=CA/ST=QC/O=Company" \ + -newkey rsa:2048 -keyout /etc/ssl/private/localhost.key \ + -out /etc/ssl/certs/localhost.crt; + +# add dhparam.pem +# this step takes quite some time +RUN openssl dhparam -out /etc/ssl/dhparam.pem 4096 + +# copy config files that handle encryption to docker +WORKDIR ${NGINX_CONFIG} +COPY ./self-signed.conf ./ssl-params.conf ./certificate.conf ./ + + +# use custom uwsgi-nginx-entrypoint.sh +# this uwsgi-nginx-entrypoint.sh file is derived from: https://github.com/tiangolo/uwsgi-nginx-flask-docker/blob/master/docker-images/entrypoint.sh +# we have to modify it so that we could generate a different /etc/nginx/conf.d/nginx.conf file +WORKDIR ${ROOT} +COPY ./uwsgi-nginx-entrypoint.sh ./entrypoint2.sh +COPY ./uwsgi-nginx-entrypoint.sh ./uwsgi-nginx-entrypoint2.sh +RUN chmod +x uwsgi-nginx-entrypoint2.sh +RUN chmod +x entrypoint2.sh +RUN chown -R nginx /uwsgi-nginx-entrypoint2.sh +RUN chown -R nginx /entrypoint2.sh + +# install poetry +RUN pip install --no-cache-dir "poetry==$POETRY_VERSION" + +# set work directory +WORKDIR ${APP_PARENT_DIR} +RUN chown www-data:www-data ${APP_PARENT_DIR} + +# remove the old uwsgi.ini and main.py from the original image +RUN rm -rf ${APP_PARENT_DIR}/main.py +RUN rm -rf ${APP_PARENT_DIR}/uwsgi.ini + +# copy to use custom uwsgi.ini +COPY ./uwsgi.ini ./ + +# create a separate folder called app +RUN mkdir app +WORKDIR ${APP_DIR} + +# copy other files to app/app +# Note: run_api.py is not needed + +COPY ./pyproject.toml ./poetry.lock ./main.py ./ +COPY ./config_example.yml ./config.yml +RUN poetry config virtualenvs.create false +RUN poetry install --no-interaction --all-extras --no-root + +# copy schematic_api folder +COPY schematic_api ./schematic_api + +# copy great_expectations folder +COPY great_expectations ./great_expectations + +# copy tests folder because some endpoints by default download to the tests folder +COPY tests ./tests + +# change permission +RUN chown -R www-data:www-data ${APP_DIR} + +# allow downloading to synapse cache +RUN chown -R www-data:www-data /root + +# copy schematic +COPY schematic ./schematic + +# change permission +WORKDIR /var/www/ +#The -R option: make the command recursive, so it will change the owner of all files and subdirectories within a given folder. +RUN chown -R www-data:www-data /var/www/ + +RUN chown -R www-data:www-data /var/tmp/ + +# change work directory back +WORKDIR ${APP_DIR} + +# specify entrypoint again to generate config +# have to respecify CMD too +ENTRYPOINT ["/entrypoint2.sh"] +CMD ["/start.sh"] + +# Expose ports +EXPOSE 443 diff --git a/schematic_api/api/__init__.py b/schematic_api/api/__init__.py index 82bad7e9b..a65398ee5 100644 --- a/schematic_api/api/__init__.py +++ b/schematic_api/api/__init__.py @@ -1,13 +1,34 @@ import os import connexion +from typing import Tuple + +import traceback +from synapseclient.core.exceptions import ( + SynapseAuthenticationError, +) +from schematic.exceptions import AccessCredentialsError from schematic import CONFIG +from jaeger_client import Config +from flask_opentracing import FlaskTracer + +config = Config( + config={ + "enabled": True, + "sampler": {"type": "const", "param": 1}, + "logging": True, + }, + service_name="schema-api", +) +jaeger_tracer = config.initialize_tracer + def create_app(): connexionapp = connexion.FlaskApp(__name__, specification_dir="openapi/") - connexionapp.add_api("api.yaml", arguments={"title": "Schematic REST API"}, pythonic_params=True) - + connexionapp.add_api( + "api.yaml", arguments={"title": "Schematic REST API"}, pythonic_params=True + ) # get the underlying Flask app instance app = connexionapp.app @@ -20,22 +41,43 @@ def create_app(): app.config["SCHEMATIC_CONFIG"] = schematic_config app.config["SCHEMATIC_CONFIG_CONTENT"] = schematic_config_content - # Configure flask app - # app.config[] = schematic[] - # app.config[] = schematic[] - # app.config[] = schematic[] + # handle exceptions in schematic when an exception gets raised + @app.errorhandler(Exception) + def handle_exception(e: Exception) -> Tuple[str, int]: + """handle exceptions in schematic APIs""" + # Ensure the application context is available + with app.app_context(): + # Get the last line of error from the traceback + last_line = traceback.format_exc().strip().split("\n")[-1] + + # Log the full trace + app.logger.error(traceback.format_exc()) - # Initialize extension schematic - # import MyExtension - # myext = MyExtension() - # myext.init_app(app) + # Return a JSON response with the last line of the error + return last_line, 500 + + @app.errorhandler(SynapseAuthenticationError) + def handle_synapse_auth_error(e: Exception) -> Tuple[str, int]: + """handle synapse authentication error""" + return str(e), 401 + + @app.errorhandler(AccessCredentialsError) + def handle_synapse_access_error(e: Exception) -> Tuple[str, int]: + """handle synapse access error""" + return str(e), 403 return app + app = create_app() +flask_tracer = FlaskTracer( + jaeger_tracer, True, app, ["url", "url_rule", "environ.HTTP_X_REAL_IP", "path"] +) + # def route_code(): # import flask_schematic as sc # sc.method1() -# \ No newline at end of file +# ] +# diff --git a/schematic_api/api/__main__.py b/schematic_api/api/__main__.py index 923cebaf5..afc24b44a 100644 --- a/schematic_api/api/__main__.py +++ b/schematic_api/api/__main__.py @@ -2,7 +2,7 @@ from schematic_api.api import app -def main(): +def main(): # Get app configuration host = os.environ.get("APP_HOST", "0.0.0.0") port = os.environ.get("APP_PORT", "3001") @@ -11,5 +11,6 @@ def main(): # Launch app app.run(host=host, port=port, debug=False) + if __name__ == "__main__": - main() \ No newline at end of file + main() diff --git a/schematic_api/api/routes.py b/schematic_api/api/routes.py index fbf36fbf5..b2439133e 100644 --- a/schematic_api/api/routes.py +++ b/schematic_api/api/routes.py @@ -19,7 +19,18 @@ import pandas as pd import json -from typing import Optional +from typing import Optional, List, Any +from functools import wraps + +from opentelemetry import trace +from opentelemetry.sdk.trace import TracerProvider +from opentelemetry.sdk.resources import SERVICE_NAME, Resource +from opentelemetry.sdk.trace.export import ( + BatchSpanProcessor, + ConsoleSpanExporter, + Span, +) +from opentelemetry.exporter.otlp.proto.http.trace_exporter import OTLPSpanExporter from schematic.configuration.configuration import CONFIG from schematic.visualization.attributes_explorer import AttributesExplorer @@ -39,11 +50,71 @@ SynapseTimeoutError, ) from schematic.utils.general import entity_type_mapping -from schematic.utils.schema_utils import get_property_label_from_display_name, DisplayLabelType +from schematic.utils.schema_utils import ( + get_property_label_from_display_name, + DisplayLabelType, +) +from schematic.utils.schema_utils import ( + get_property_label_from_display_name, + DisplayLabelType, +) logger = logging.getLogger(__name__) logging.basicConfig(level=logging.DEBUG) +trace.set_tracer_provider( + TracerProvider(resource=Resource(attributes={SERVICE_NAME: "schematic-api"})) +) + + +# borrowed from: https://github.com/Sage-Bionetworks/synapsePythonClient/blob/develop/tests/integration/conftest.py +class FileSpanExporter(ConsoleSpanExporter): + """Create an exporter for OTEL data to a file.""" + + def __init__(self, file_path: str) -> None: + """Init with a path.""" + self.file_path = file_path + + def export(self, spans: List[Span]) -> None: + """Export the spans to the file.""" + with open(self.file_path, "a", encoding="utf-8") as f: + for span in spans: + span_json_one_line = span.to_json().replace("\n", "") + "\n" + f.write(span_json_one_line) + + +trace.get_tracer_provider().add_span_processor(BatchSpanProcessor(OTLPSpanExporter())) +# processor = SimpleSpanProcessor(FileSpanExporter("otel_spans_schemati_api.json")) +# trace.get_tracer_provider().add_span_processor(processor) +tracer = trace.get_tracer("Schematic") + + +def trace_function_params(): + """capture all the parameters of API requests""" + + def decorator(func): + """create a decorator""" + + @wraps(func) + def wrapper(*args, **kwargs): + """create a wrapper function. Any number of positional arguments and keyword arguments can be passed here.""" + tracer = trace.get_tracer(__name__) + # Start a new span with the function's name + with tracer.start_as_current_span(func.__name__) as span: + # Set values of parameters as tags + for i, arg in enumerate(args): + span.set_attribute(f"arg{i}", arg) + + for name, value in kwargs.items(): + span.set_attribute(name, value) + # Call the actual function + result = func(*args, **kwargs) + return result + + return wrapper + + return decorator + def config_handler(asset_view: str = None): # check if path to config is provided @@ -210,6 +281,7 @@ def save_file(file_key="csv_file"): return temp_path + def initalize_metadata_model(schema_url, data_model_labels): # get path to temp data model file (csv or jsonld) as appropriate data_model = get_temp_model_path(schema_url) @@ -259,6 +331,7 @@ def get_temp_model_path(schema_url): # @before_request +@trace_function_params() def get_manifest_route( schema_url: str, use_annotations: bool, @@ -283,7 +356,6 @@ def get_manifest_route( Returns: Googlesheet URL (if sheet_url is True), or pandas dataframe (if sheet_url is False). """ - # Get access token from request header access_token = get_access_token() @@ -322,8 +394,7 @@ def get_manifest_route( return all_results -#####profile validate manifest route function -# @profile(sort_by='cumulative', strip_dirs=True) +@trace_function_params() def validate_manifest_route( schema_url, data_type, @@ -380,7 +451,7 @@ def validate_manifest_route( #####profile validate manifest route function -# @profile(sort_by='cumulative', strip_dirs=True) +@trace_function_params() def submit_manifest_route( schema_url, data_model_labels: str, @@ -393,7 +464,7 @@ def submit_manifest_route( project_scope=None, table_column_names=None, annotation_keys=None, - file_annotations_upload:bool=True, + file_annotations_upload: bool = True, ): # call config_handler() config_handler(asset_view=asset_view) @@ -450,7 +521,7 @@ def submit_manifest_route( project_scope=project_scope, table_column_names=table_column_names, annotation_keys=annotation_keys, - file_annotations_upload=file_annotations_upload + file_annotations_upload=file_annotations_upload, ) return manifest_id @@ -675,7 +746,6 @@ def download_manifest(manifest_id, new_manifest_name="", as_json=True): return manifest_local_file_path -# @profile(sort_by='cumulative', strip_dirs=True) def download_dataset_manifest(dataset_id, asset_view, as_json, new_manifest_name=""): # Access token now stored in request header access_token = get_access_token() @@ -729,6 +799,7 @@ def get_asset_view_table(asset_view, return_type): file_view_table_df.to_csv(export_path, index=False) return export_path + def get_project_manifests(project_id, asset_view): # Access token now stored in request header access_token = get_access_token() @@ -1022,4 +1093,4 @@ def get_schematic_version() -> str: raise NotImplementedError( "Using this endpoint to check the version of schematic is only supported when the API is running in a docker container." ) - return version \ No newline at end of file + return version diff --git a/schematic_api/api/security_controller_.py b/schematic_api/api/security_controller_.py index ee336dcb0..fbde596bb 100644 --- a/schematic_api/api/security_controller_.py +++ b/schematic_api/api/security_controller_.py @@ -11,4 +11,4 @@ def info_from_bearerAuth(token): :return: Decoded token information or None if token is invalid :rtype: dict | None """ - return {"uid": "user_id"} \ No newline at end of file + return {"uid": "user_id"} diff --git a/tests/conftest.py b/tests/conftest.py index 5e19933b3..62c2cb3e3 100644 --- a/tests/conftest.py +++ b/tests/conftest.py @@ -1,18 +1,15 @@ -from multiprocessing.sharedctypes import Value +"""Fixtures and helpers for use across all tests""" import os import logging import sys +from typing import Generator import shutil import pytest -import pandas as pd -from dotenv import load_dotenv, find_dotenv -from time import perf_counter +from dotenv import load_dotenv from schematic.schemas.data_model_parser import DataModelParser from schematic.schemas.data_model_graph import DataModelGraph, DataModelGraphExplorer -from schematic.schemas.data_model_nodes import DataModelNodes -from schematic.schemas.data_model_json_schema import DataModelJSONSchema from schematic.configuration.configuration import CONFIG from schematic.utils.df_utils import load_df @@ -128,3 +125,27 @@ def synapse_store(request): synapse_store = SynapseStorage() yield synapse_store + + +# These fixtures make copies of existing test manifests. +# These copies can the be altered by a given test, and the copy will eb destroyed at the +# end of the test + + +@pytest.fixture(scope="function") +def temporary_file_copy(request, helpers: Helpers) -> Generator[str, None, None]: + file_name = request.param + # original file copy + original_test_path = helpers.get_data_path(f"mock_manifests/{file_name}") + # get filename without extension + file_name_no_extension = file_name.split(".")[0] + # Copy the original CSV file to a temporary directory + temp_csv_path = helpers.get_data_path( + f"mock_manifests/{file_name_no_extension}_copy.csv" + ) + + shutil.copyfile(original_test_path, temp_csv_path) + yield temp_csv_path + # Teardown + if os.path.exists(temp_csv_path): + os.remove(temp_csv_path) diff --git a/tests/data/test_configs/default_config.yml b/tests/data/test_configs/default_config.yml index 6775b569a..5a1785dc2 100644 --- a/tests/data/test_configs/default_config.yml +++ b/tests/data/test_configs/default_config.yml @@ -16,6 +16,5 @@ model: location: 'tests/data/example.model.jsonld' google_sheets: - service_acct_creds_synapse_id: 'syn25171627' service_acct_creds: "schematic_service_account_creds.json" strict_validation: true diff --git a/tests/data/test_configs/valid_config.yml b/tests/data/test_configs/valid_config.yml index 3e340721c..456c3ccd7 100644 --- a/tests/data/test_configs/valid_config.yml +++ b/tests/data/test_configs/valid_config.yml @@ -16,6 +16,5 @@ model: location: "model.jsonld" google_sheets: - service_acct_creds_synapse_id: "syn1" service_acct_creds: "creds.json" strict_validation: false diff --git a/tests/data/test_configs/valid_config2.yml b/tests/data/test_configs/valid_config2.yml index 78306ee18..e1c85ab4a 100644 --- a/tests/data/test_configs/valid_config2.yml +++ b/tests/data/test_configs/valid_config2.yml @@ -10,6 +10,5 @@ model: location: "model.jsonld" google_sheets: - service_acct_creds_synapse_id: "syn1" service_acct_creds: "creds.json" strict_validation: false diff --git a/tests/test_api.py b/tests/test_api.py index a070297ab..97183186f 100644 --- a/tests/test_api.py +++ b/tests/test_api.py @@ -78,7 +78,7 @@ def test_manifest_json(helpers): @pytest.fixture(scope="class") def data_model_jsonld(): - data_model_jsonld ="https://raw.githubusercontent.com/Sage-Bionetworks/schematic/develop/tests/data/example.model.jsonld" + data_model_jsonld = "https://raw.githubusercontent.com/Sage-Bionetworks/schematic/develop/tests/data/example.model.jsonld" yield data_model_jsonld @@ -132,8 +132,30 @@ def request_headers(syn_token): yield headers +@pytest.fixture +def request_invalid_headers(): + headers = {"Authorization": "Bearer invalid headers"} + yield headers + + @pytest.mark.schematic_api class TestSynapseStorage: + def test_invalid_authentication(self, client, request_invalid_headers): + response = client.get( + "http://localhost:3001/v1/storage/assets/tables", + query_string={"asset_view": "syn23643253", "return_type": "csv"}, + headers=request_invalid_headers, + ) + assert response.status_code == 401 + + def test_insufficent_auth(self, client, request_headers): + response = client.get( + "http://localhost:3001/v1/storage/assets/tables", + query_string={"asset_view": "syn23643252", "return_type": "csv"}, + headers=request_headers, + ) + assert response.status_code == 403 + @pytest.mark.synapse_credentials_needed @pytest.mark.parametrize("return_type", ["json", "csv"]) def test_get_storage_assets_tables(self, client, return_type, request_headers): @@ -348,8 +370,7 @@ def test_get_property_label_from_display_name(self, client, strict_camel_case): @pytest.mark.schematic_api class TestDataModelGraphExplorerOperation: def test_get_schema(self, client, data_model_jsonld): - params = {"schema_url": data_model_jsonld, - "data_model_labels": 'class_label'} + params = {"schema_url": data_model_jsonld, "data_model_labels": "class_label"} response = client.get( "http://localhost:3001/v1/schemas/get/schema", query_string=params ) @@ -363,7 +384,11 @@ def test_get_schema(self, client, data_model_jsonld): os.remove(response_dt) def test_if_node_required(test, client, data_model_jsonld): - params = {"schema_url": data_model_jsonld, "node_display_name": "FamilyHistory", "data_model_labels": "class_label"} + params = { + "schema_url": data_model_jsonld, + "node_display_name": "FamilyHistory", + "data_model_labels": "class_label", + } response = client.get( "http://localhost:3001/v1/schemas/is_node_required", query_string=params @@ -791,6 +816,19 @@ def test_generate_manifest_not_file_based_with_annotations( ] ) + def test_generate_manifest_data_type_not_found(self, client, data_model_jsonld): + params = { + "schema_url": data_model_jsonld, + "data_type": "wrong data type", + "use_annotations": False, + } + response = client.get( + "http://localhost:3001/v1/manifest/generate", query_string=params + ) + + assert response.status_code == 500 + assert "LookupError" in str(response.data) + def test_populate_manifest(self, client, data_model_jsonld, test_manifest_csv): # test manifest test_manifest_data = open(test_manifest_csv, "rb") @@ -1086,7 +1124,11 @@ def test_submit_manifest_file_only_replace( elif python_version == "3.9": dataset_id = "syn52656104" - specific_params = {"asset_view": "syn23643253", "dataset_id": dataset_id, "project_scope":["syn54126707"]} + specific_params = { + "asset_view": "syn23643253", + "dataset_id": dataset_id, + "project_scope": ["syn54126707"], + } params.update(specific_params) diff --git a/tests/test_configuration.py b/tests/test_configuration.py index 8845a9b48..7a27c7a34 100644 --- a/tests/test_configuration.py +++ b/tests/test_configuration.py @@ -80,7 +80,6 @@ def test_google_sheets_config(self) -> None: assert isinstance( GoogleSheetsConfig( service_acct_creds="file_name", - service_acct_creds_synapse_id="syn1", strict_validation=True, ), GoogleSheetsConfig, @@ -88,19 +87,11 @@ def test_google_sheets_config(self) -> None: with pytest.raises(ValidationError): GoogleSheetsConfig( service_acct_creds="file_name", - service_acct_creds_synapse_id="syn1", strict_validation="tru", ) with pytest.raises(ValidationError): GoogleSheetsConfig( service_acct_creds="", - service_acct_creds_synapse_id="syn1", - strict_validation=True, - ) - with pytest.raises(ValidationError): - GoogleSheetsConfig( - service_acct_creds="file_name", - service_acct_creds_synapse_id="syn", strict_validation=True, ) @@ -120,7 +111,6 @@ def test_init(self) -> None: assert config.manifest_title == "example" assert config.manifest_data_type == ["Biospecimen", "Patient"] assert config.model_location == "tests/data/example.model.jsonld" - assert config.service_account_credentials_synapse_id assert ( config.service_account_credentials_path != "schematic_service_account_creds.json" @@ -158,7 +148,6 @@ def test_load_config1(self) -> None: assert config.manifest_title == "example" assert config.manifest_data_type == ["Biospecimen", "Patient"] assert config.model_location == "tests/data/example.model.jsonld" - assert config.service_account_credentials_synapse_id assert ( config.service_account_credentials_path != "schematic_service_account_creds.json" @@ -188,7 +177,6 @@ def test_load_config2(self) -> None: assert config.manifest_title == "title" assert config.manifest_data_type == ["data_type"] assert config.model_location == "model.jsonld" - assert config.service_account_credentials_synapse_id assert os.path.basename(config.service_account_credentials_path) == "creds.json" assert config.google_sheets_master_template_id == ( "1LYS5qE4nV9jzcYw5sXwCza25slDfRA1CIg3cs-hCdpU" diff --git a/tests/test_manifest.py b/tests/test_manifest.py index 0525b6c6a..c34148dab 100644 --- a/tests/test_manifest.py +++ b/tests/test_manifest.py @@ -61,7 +61,9 @@ def manifest_generator(helpers, request): # Get graph data model graph_data_model = generate_graph_data_model( - helpers, path_to_data_model=path_to_data_model, data_model_labels='class_label', + helpers, + path_to_data_model=path_to_data_model, + data_model_labels="class_label", ) manifest_generator = ManifestGenerator( @@ -111,18 +113,22 @@ def manifest(dataset_id, manifest_generator, request): yield manifest, use_annotations, data_type, sheet_url + @pytest.fixture(scope="class") def app(): app = create_app() yield app + class TestManifestGenerator: def test_init(self, helpers): path_to_data_model = helpers.get_data_path("example.model.jsonld") # Get graph data model graph_data_model = generate_graph_data_model( - helpers, path_to_data_model=path_to_data_model, data_model_labels='class_label', + helpers, + path_to_data_model=path_to_data_model, + data_model_labels="class_label", ) generator = ManifestGenerator( @@ -157,7 +163,9 @@ def test_missing_root_error(self, helpers, data_type, exc, exc_message): # Get graph data model graph_data_model = generate_graph_data_model( - helpers, path_to_data_model=path_to_data_model, data_model_labels='class_label', + helpers, + path_to_data_model=path_to_data_model, + data_model_labels="class_label", ) # A LookupError should be raised and include message when the component cannot be found @@ -242,7 +250,9 @@ def test_get_manifest_excel(self, helpers, sheet_url, output_format, dataset_id) # Get graph data model graph_data_model = generate_graph_data_model( - helpers, path_to_data_model=path_to_data_model, data_model_labels='class_label', + helpers, + path_to_data_model=path_to_data_model, + data_model_labels="class_label", ) generator = ManifestGenerator( @@ -300,7 +310,9 @@ def test_get_manifest_no_annos(self, helpers, dataset_id): # Get graph data model graph_data_model = generate_graph_data_model( - helpers, path_to_data_model=path_to_data_model, data_model_labels='class_label', + helpers, + path_to_data_model=path_to_data_model, + data_model_labels="class_label", ) # Instantiate object with use_annotations set to True @@ -416,7 +428,9 @@ def test_add_root_to_component_without_additional_metadata( # Get graph data model graph_data_model = generate_graph_data_model( - helpers, path_to_data_model=path_to_data_model, data_model_labels='class_label', + helpers, + path_to_data_model=path_to_data_model, + data_model_labels="class_label", ) manifest_generator = ManifestGenerator( @@ -453,7 +467,9 @@ def test_add_root_to_component_with_additional_metadata( # Get graph data model graph_data_model = generate_graph_data_model( - helpers, path_to_data_model=path_to_data_model, data_model_labels='class_label', + helpers, + path_to_data_model=path_to_data_model, + data_model_labels="class_label", ) manifest_generator = ManifestGenerator( @@ -537,7 +553,9 @@ def test_update_dataframe_with_existing_df(self, helpers, existing_manifest): # Get graph data model graph_data_model = generate_graph_data_model( - helpers, path_to_data_model=path_to_data_model, data_model_labels='class_label', + helpers, + path_to_data_model=path_to_data_model, + data_model_labels="class_label", ) # Instantiate the Manifest Generator. @@ -661,34 +679,123 @@ def test_populate_existing_excel_spreadsheet( # remove file os.remove(dummy_output_path) - - @pytest.mark.parametrize("return_output", ["Mock excel file path", "Mock google sheet link"]) - def test_create_single_manifest(self, simple_manifest_generator, helpers, return_output): - with patch("schematic.manifest.generator.ManifestGenerator.get_manifest", return_value=return_output): + + @pytest.mark.parametrize( + "return_output", ["Mock excel file path", "Mock google sheet link"] + ) + def test_create_single_manifest( + self, simple_manifest_generator, helpers, return_output + ): + with patch( + "schematic.manifest.generator.ManifestGenerator.get_manifest", + return_value=return_output, + ): json_ld_path = helpers.get_data_path("example.model.jsonld") data_type = "Patient" - graph_data_model = generate_graph_data_model(helpers, path_to_data_model=json_ld_path, data_model_labels='class_label') + graph_data_model = generate_graph_data_model( + helpers, + path_to_data_model=json_ld_path, + data_model_labels="class_label", + ) - result = simple_manifest_generator.create_single_manifest(path_to_data_model=json_ld_path, graph_data_model=graph_data_model, data_type=data_type, output_format="google_sheet", use_annotations=False) + result = simple_manifest_generator.create_single_manifest( + path_to_data_model=json_ld_path, + graph_data_model=graph_data_model, + data_type=data_type, + output_format="google_sheet", + use_annotations=False, + ) assert result == return_output - - @pytest.mark.parametrize("test_data_types", [["Patient", "Biospecimen"], ["all manifests"]]) - def test_create_manifests_raise_errors(self, simple_manifest_generator, helpers, test_data_types): - with pytest.raises(ValueError) as exception_info: + + @pytest.mark.parametrize( + "test_data_types", [["Patient", "Biospecimen"], ["all manifests"]] + ) + def test_create_manifests_raise_errors( + self, simple_manifest_generator, helpers, test_data_types + ): + with pytest.raises(ValueError) as exception_info: json_ld_path = helpers.get_data_path("example.model.jsonld") data_types = test_data_types - dataset_ids=["syn123456"] - - simple_manifest_generator.create_manifests(path_to_data_model=json_ld_path, data_types=data_types, dataset_ids=dataset_ids, output_format="google_sheet", use_annotations=False, data_model_labels='class_label') - - @pytest.mark.parametrize("test_data_types, dataset_ids, expected_result", [ - (["Patient", "Biospecimen"], ["mock dataset id1", "mock dataset id2"], ["mock google sheet link", "mock google sheet link"]), - (["Patient"], ["mock dataset id1"], ["mock google sheet link"]), - ]) - def test_create_manifests(self, simple_manifest_generator, helpers, test_data_types, dataset_ids, expected_result): - with patch("schematic.manifest.generator.ManifestGenerator.create_single_manifest", return_value="mock google sheet link"): + dataset_ids = ["syn123456"] + + simple_manifest_generator.create_manifests( + path_to_data_model=json_ld_path, + data_types=data_types, + dataset_ids=dataset_ids, + output_format="google_sheet", + use_annotations=False, + data_model_labels="class_label", + ) + + @pytest.mark.parametrize( + "test_data_types, dataset_ids, expected_result", + [ + ( + ["Patient", "Biospecimen"], + ["mock dataset id1", "mock dataset id2"], + ["mock google sheet link", "mock google sheet link"], + ), + (["Patient"], ["mock dataset id1"], ["mock google sheet link"]), + ], + ) + def test_create_manifests( + self, + simple_manifest_generator, + helpers, + test_data_types, + dataset_ids, + expected_result, + ): + with patch( + "schematic.manifest.generator.ManifestGenerator.create_single_manifest", + return_value="mock google sheet link", + ): json_ld_path = helpers.get_data_path("example.model.jsonld") - all_results = simple_manifest_generator.create_manifests(path_to_data_model=json_ld_path, data_types=test_data_types, dataset_ids=dataset_ids, output_format="google_sheet", use_annotations=False, data_model_labels='class_label') + all_results = simple_manifest_generator.create_manifests( + path_to_data_model=json_ld_path, + data_types=test_data_types, + dataset_ids=dataset_ids, + output_format="google_sheet", + use_annotations=False, + data_model_labels="class_label", + ) assert all_results == expected_result - + + @pytest.mark.parametrize( + "component,datasetId", + [("Biospecimen", "syn61260107"), ("BulkRNA-seqAssay", "syn61374924")], + ids=["Record based", "File based"], + ) + def test_get_manifest_with_files(self, helpers, component, datasetId): + """ + Test to ensure that when generating a record based manifset that has files in the dataset that the files are not added to the manifest as well + """ + path_to_data_model = helpers.get_data_path("example.model.jsonld") + + graph_data_model = generate_graph_data_model( + helpers, + path_to_data_model=path_to_data_model, + data_model_labels="class_label", + ) + + generator = ManifestGenerator( + path_to_data_model=path_to_data_model, + graph=graph_data_model, + root=component, + use_annotations=True, + ) + + manifest = generator.get_manifest( + dataset_id=datasetId, output_format="dataframe" + ) + + filename_in_manifest_columns = "Filename" in manifest.columns + n_rows = manifest.shape[0] + + if component == "Biospecimen": + assert not filename_in_manifest_columns + assert n_rows == 4 + elif component == "BulkRNA-seqAssay": + assert filename_in_manifest_columns + assert n_rows == 3 diff --git a/tests/test_metadata.py b/tests/test_metadata.py index 7807e1129..bf0c4d97b 100644 --- a/tests/test_metadata.py +++ b/tests/test_metadata.py @@ -1,6 +1,7 @@ +"""Tests for Metadata class""" + import logging import os -import shutil from typing import Optional, Generator from pathlib import Path from unittest.mock import patch @@ -24,28 +25,6 @@ def metadata_model(helpers, data_model_labels): return metadata_model -@pytest.fixture -def test_bulkrnaseq(helpers: Helpers) -> Generator[Path, None, None]: - """create temporary copy of test_BulkRNAseq.csv - This fixture creates a temporary copy of the original 'test_BulkRNAseq.csv' file - After test, the copied file is removed. - Args: - helpers (Helpers): Helpers fixture - - Yields: - Generator[Path, None, None]: temporary file path of the copied version test_BulkRNAseq.csv - """ - # original bulkrnaseq csv - original_test_path = helpers.get_data_path("mock_manifests/test_BulkRNAseq.csv") - # Copy the original CSV file to a temporary directory - temp_csv_path = helpers.get_data_path("mock_manifests/test_BulkRNAseq2.csv") - shutil.copyfile(original_test_path, temp_csv_path) - yield temp_csv_path - # Teardown - if os.path.exists(temp_csv_path): - os.remove(temp_csv_path) - - class TestMetadataModel: @pytest.mark.parametrize("as_graph", [True, False], ids=["as_graph", "as_list"]) @pytest.mark.parametrize( @@ -130,9 +109,12 @@ def test_populate_manifest(self, helpers, return_excel, data_model_labels): ids=["data_model_labels-display_label", "data_model_labels-class_label"], ) @pytest.mark.parametrize("validate_component", [None, "BulkRNA-seqAssay"]) + @pytest.mark.parametrize( + "temporary_file_copy", ["test_BulkRNAseq.csv"], indirect=True + ) def test_submit_metadata_manifest( self, - test_bulkrnaseq: Path, + temporary_file_copy: Generator[str, None, None], helpers: Helpers, file_annotations_upload: bool, restrict_rules: bool, @@ -149,7 +131,8 @@ def test_submit_metadata_manifest( "schematic.store.synapse.SynapseStorage.associateMetadataWithFiles", return_value="mock manifest id", ): - mock_manifest_path = test_bulkrnaseq + mock_manifest_path = temporary_file_copy + mock_manifest_id = meta_data_model.submit_metadata_manifest( manifest_path=mock_manifest_path, validate_component=validate_component, diff --git a/tests/test_schemas.py b/tests/test_schemas.py index 85aa4cabe..f80449b18 100644 --- a/tests/test_schemas.py +++ b/tests/test_schemas.py @@ -20,6 +20,7 @@ convert_bool_to_str, parse_validation_rules, DisplayLabelType, + get_json_schema_log_file_path, ) from schematic.utils.io_utils import load_json @@ -447,9 +448,12 @@ def test_generate_data_model_graph(self, helpers, data_model, data_model_labels) # Check that all relationships recorded between 'CheckList' and 'Ab' are present assert ( - "rangeValue" and "parentOf" in graph["CheckListEnum"][expected_valid_values[0]] + "rangeValue" + and "parentOf" in graph["CheckListEnum"][expected_valid_values[0]] + ) + assert ( + "requiresDependency" not in graph["CheckListEnum"][expected_valid_values[0]] ) - assert "requiresDependency" not in graph["CheckListEnum"][expected_valid_values[0]] # Check nodes: assert "Patient" in graph.nodes @@ -987,10 +991,7 @@ def test_generate_node_dict( # Check that the display name matches the label if data_model_labels == "display_label": - try: - assert node_display_name == node_dict["label"] - except: - breakpoint() + assert node_display_name == node_dict["label"] def test_generate_node(self, helpers, data_model): # Test adding a dummy node @@ -1296,6 +1297,7 @@ def test_get_non_blank_schema(self, helpers, data_model, node_name): @pytest.mark.parametrize("blank", [True, False], ids=["True_blank", "False_blank"]) def test_get_range_schema(self, helpers, data_model, node_range, node_name, blank): dmjs = get_data_model_json_schema(helpers=helpers, data_model_name=data_model) + range_schema = dmjs.get_range_schema( node_range=node_range, node_name=node_name, blank=blank ) @@ -1324,6 +1326,16 @@ def test_get_json_validation_schema( ): dmjs = get_data_model_json_schema(helpers=helpers, data_model_name=data_model) + data_model_path = helpers.get_data_path(path=data_model) + json_schema_log_file_path = get_json_schema_log_file_path( + data_model_path=data_model_path, source_node=source_node + ) + + # Remove json schema log file if it already exists. + if os.path.exists(json_schema_log_file_path): + os.remove(json_schema_log_file_path) + assert os.path.exists(json_schema_log_file_path) == False + try: # Get validation schema json_validation_schema = dmjs.get_json_validation_schema( @@ -1349,6 +1361,13 @@ def test_get_json_validation_schema( # Check contents of validation schema assert "Diagnosis" in json_validation_schema["properties"] assert "Cancer" in json_validation_schema["properties"]["Diagnosis"]["enum"] + + # Check that log file is saved + assert os.path.exists(json_schema_log_file_path) == True + + # Remove the log file that was created. + os.remove(json_schema_log_file_path) + except: # Should only fail if no source node is provided. assert source_node == "" diff --git a/tests/test_store.py b/tests/test_store.py index c2038db76..5ac61f3d0 100644 --- a/tests/test_store.py +++ b/tests/test_store.py @@ -22,11 +22,7 @@ from tests.conftest import Helpers from schematic.store.base import BaseStorage -from schematic.store.synapse import ( - DatasetFileView, - ManifestDownload, - SynapseStorage -) +from schematic.store.synapse import DatasetFileView, ManifestDownload, SynapseStorage from schematic.utils.general import check_synapse_cache_size logging.basicConfig(level=logging.DEBUG) @@ -131,7 +127,7 @@ def test_init(self): class TestSynapseStorage: "Tests the SynapseStorage class" - def test_init(self, synapse_store:SynapseStorage) -> None: + def test_init(self, synapse_store: SynapseStorage) -> None: """Tests SynapseStorage.__init__""" assert synapse_store.storageFileview == "syn23643253" assert isinstance(synapse_store.storageFileviewTable, pd.DataFrame) @@ -142,8 +138,7 @@ def test__purge_synapse_cache(self) -> None: synapse_store = SynapseStorage(synapse_cache_path="test_cache_dir") size_before_purge = check_synapse_cache_size(synapse_store.root_synapse_cache) synapse_store._purge_synapse_cache( - maximum_storage_allowed_cache_gb=0.000001, - minute_buffer=0 + maximum_storage_allowed_cache_gb=0.000001, minute_buffer=0 ) size_after_purge = check_synapse_cache_size(synapse_store.root_synapse_cache) assert size_before_purge > size_after_purge @@ -157,7 +152,7 @@ def test_login(self) -> None: assert synapse_client.cache.cache_root_dir == "test_cache_dir" shutil.rmtree("test_cache_dir") - def test_getFileAnnotations(self, synapse_store:SynapseStorage) -> None: + def test_getFileAnnotations(self, synapse_store: SynapseStorage) -> None: expected_dict = { "author": "bruno, milen, sujay", "impact": "42.9", @@ -214,45 +209,46 @@ def test_get_file_entityIds(self, helpers, synapse_store, only_new_files): assert len(files_and_Ids["entityId"]) == 2 @pytest.mark.parametrize( - "manifest_path, test_annotations, datasetId, manifest_record_type", + "test_annotations, dataset_id, manifest_record_type, temporary_file_copy", [ ( - "mock_manifests/annotations_test_manifest.csv", {"CheckInt": "7", "CheckList": "valid, list, values"}, "syn34295552", "file_and_entities", + "annotations_test_manifest.csv", ), ( - "mock_manifests/test_BulkRNAseq.csv", {"FileFormat": "BAM", "GenomeBuild": "GRCh38"}, "syn39241199", "table_and_file", + "test_BulkRNAseq.csv", ), ], ids=["non file-based", "file-based"], + indirect=["temporary_file_copy"], ) def test_annotation_submission( self, - synapse_store, + synapse_store: SynapseStorage, helpers, - manifest_path, - test_annotations, - datasetId, - manifest_record_type, - config: Configuration, + test_annotations: dict[str, str], + dataset_id: str, + manifest_record_type: str, dmge: DataModelGraphExplorer, + temporary_file_copy: Generator[str, None, None], ): - manifest_id = synapse_store.associateMetadataWithFiles( + """Test annotation submission""" + synapse_store.associateMetadataWithFiles( dmge=dmge, - metadataManifestPath=helpers.get_data_path(manifest_path), - datasetId=datasetId, + metadataManifestPath=temporary_file_copy, + datasetId=dataset_id, manifest_record_type=manifest_record_type, hideBlanks=True, restrict_manifest=False, ) # Retrive annotations - entity_id = helpers.get_data_frame(manifest_path)["entityId"][0] + entity_id = helpers.get_data_frame(temporary_file_copy)["entityId"][0] annotations = synapse_store.getFileAnnotations(entity_id) # Check annotations of interest @@ -260,11 +256,11 @@ def test_annotation_submission( assert key in annotations.keys() assert annotations[key] == test_annotations[key] - if manifest_path.endswith("annotations_test_manifest.csv"): + if temporary_file_copy.endswith("annotations_test_manifest_copy.csv"): assert "CheckRecommended" not in annotations.keys() - elif manifest_path.endswith("test_BulkRNAseq.csv"): + elif temporary_file_copy.endswith("test_BulkRNAseq_copy.csv"): entity = synapse_store.syn.get(entity_id) - assert type(entity) == File + assert isinstance(entity, File) @pytest.mark.parametrize("force_batch", [True, False], ids=["batch", "non_batch"]) def test_getDatasetAnnotations(self, dataset_id, synapse_store, force_batch): @@ -482,6 +478,7 @@ def test_get_files_metadata_from_dataset(self, synapse_store): "entityId": ["syn123", "syn456"], } + class TestDatasetFileView: def test_init(self, dataset_id, dataset_fileview, synapse_store): assert dataset_fileview.datasetId == dataset_id @@ -1017,17 +1014,32 @@ def test_upload_manifest_file( } ) with patch("synapseclient.Synapse.store") as syn_store_mock, patch( - "synapseutils.copy_functions.changeFileMetaData" - ): + "schematic.store.synapse.synapseutils.copy_functions.changeFileMetaData" + ) as mock_change_file_metadata: syn_store_mock.return_value.id = "mock manifest id" + mock_component_name = "BulkRNA-seqAssay" mock_file_path = helpers.get_data_path(mock_manifest_file_path) mock_manifest_synapse_file_id = synapse_store.upload_manifest_file( manifest=test_df, metadataManifestPath=mock_file_path, datasetId="mock dataset id", restrict_manifest=True, + component_name=mock_component_name, ) + if "censored" in mock_manifest_file_path: + file_name = ( + f"synapse_storage_manifest_{mock_component_name}_censored.csv" + ) + else: + file_name = f"synapse_storage_manifest_{mock_component_name}.csv" + assert mock_manifest_synapse_file_id == "mock manifest id" + mock_change_file_metadata.assert_called_once_with( + forceVersion=False, + syn=synapse_store.syn, + entity=syn_store_mock.return_value.id, + downloadAs=file_name, + ) @pytest.mark.parametrize("file_annotations_upload", [True, False]) @pytest.mark.parametrize("hide_blanks", [True, False]) diff --git a/tests/test_utils.py b/tests/test_utils.py index 8f6ef20e5..5b37abe6e 100644 --- a/tests/test_utils.py +++ b/tests/test_utils.py @@ -11,6 +11,7 @@ from typing import Union, Generator from _pytest.fixtures import FixtureRequest + import numpy as np import pandas as pd import pytest @@ -69,6 +70,7 @@ parse_validation_rules, extract_component_validation_rules, check_for_duplicate_components, + get_json_schema_log_file_path, ) @@ -186,6 +188,8 @@ "bio_things": {"class": "BioThings", "property": "bioThings"}, } +DATA_MODEL_DICT = {"example.model.csv": "CSV", "example.model.jsonld": "JSONLD"} + test_disk_storage = [ (2, 4000, 16000), (1000, 4000, 16000), @@ -193,7 +197,8 @@ (1073741825, 1073741824, 1181116006.4), ] -def get_metadataModel(helpers, model_name:str): + +def get_metadataModel(helpers, model_name: str): metadataModel = MetadataModel( inputMModelLocation=helpers.get_data_path(model_name), inputMModelLocationType="local", @@ -1021,6 +1026,28 @@ def test_get_label_from_display_name(self, test_dn: str, data_model_labels: str) return return + @pytest.mark.parametrize( + "data_model", list(DATA_MODEL_DICT.keys()), ids=list(DATA_MODEL_DICT.values()) + ) + @pytest.mark.parametrize( + "source_node", + ["Biospecimen", "Patient"], + ids=["biospecimen_source", "patient_source"], + ) + def test_get_json_schema_log_file_path( + self, helpers, data_model: str, source_node: str + ): + data_model_path = helpers.get_data_path(path=data_model) + json_schema_log_file_path = get_json_schema_log_file_path( + data_model_path=data_model_path, source_node=source_node + ) + + # Check that model is not included in the json_schema_log_file_path + assert ".model" not in "data_model" + + # Check the file suffixs are what is expected. + assert ["schema", "json"] == json_schema_log_file_path.split(".")[-2:] + class TestValidateUtils: def test_validate_schema(self, helpers): @@ -1074,13 +1101,22 @@ def test_validate_property_schema(self, helpers): @pytest.mark.parametrize( ("manifest", "model", "root_node"), - [("mock_manifests/Patient_test_no_entry_for_cond_required_column.manifest.csv", - "example.model.csv", "Patient"), - ("mock_manifests/Valid_Test_Manifest_with_nones.csv", - "example_test_nones.model.csv", "MockComponent")] - ) + [ + ( + "mock_manifests/Patient_test_no_entry_for_cond_required_column.manifest.csv", + "example.model.csv", + "Patient", + ), + ( + "mock_manifests/Valid_Test_Manifest_with_nones.csv", + "example_test_nones.model.csv", + "MockComponent", + ), + ], + ) def test_convert_nan_entries_to_empty_strings( - self, helpers, manifest, model, root_node): + self, helpers, manifest, model, root_node + ): # Get manifest and data model path manifest_path = helpers.get_data_path(manifest) model_path = helpers.get_data_path(model) @@ -1104,37 +1140,37 @@ def test_convert_nan_entries_to_empty_strings( manifest_path, preserve_raw_input=False, allow_na_values=True, - **load_args,) + **load_args, + ) metadataModel = get_metadataModel(helpers, model) # Instantiate Validate manifest, and run manifest validation - # In this step the manifest is modified while running rule + # In this step the manifest is modified while running rule # validation so need to do this step to get the updated manfest. - vm = ValidateManifest( - errors, manifest, manifest_path, dmge, json_schema) + vm = ValidateManifest(errors, manifest, manifest_path, dmge, json_schema) manifest, vmr_errors, vmr_warnings = vm.validate_manifest_rules( - manifest, dmge, restrict_rules=False, project_scope=["syn54126707"], + manifest, + dmge, + restrict_rules=False, + project_scope=["syn54126707"], ) # Run convert nan function - output = validate_utils.convert_nan_entries_to_empty_strings( - manifest=manifest - ) + output = validate_utils.convert_nan_entries_to_empty_strings(manifest=manifest) # Compare post rule validation manifest with output manifest looking # for expected nan to empty string conversion - if root_node == 'Patient': - assert manifest['Family History'][0] == [''] - assert output['Family History'][0] == [''] - elif root_node == 'MockComponent': - assert manifest['Check List'][2] == [''] - assert manifest['Check List Like Enum'][2] == [] - assert type(manifest['Check NA'][2]) == type(pd.NA) - - assert output['Check List'][2] == [''] - assert output['Check List Like Enum'][2] == [] - + if root_node == "Patient": + assert manifest["Family History"][0] == [""] + assert output["Family History"][0] == [""] + elif root_node == "MockComponent": + assert manifest["Check List"][2] == [""] + assert manifest["Check List Like Enum"][2] == [] + assert type(manifest["Check NA"][2]) == type(pd.NA) + + assert output["Check List"][2] == [""] + assert output["Check List Like Enum"][2] == [] def test_get_list_robustness(self, helpers): return diff --git a/tests/test_validation.py b/tests/test_validation.py index b2b85851d..9ea47b973 100644 --- a/tests/test_validation.py +++ b/tests/test_validation.py @@ -27,7 +27,8 @@ def DMGE(helpers): dmge = helpers.get_data_model_graph_explorer(path="example.model.jsonld") yield dmge -def get_metadataModel(helpers, model_name:str): + +def get_metadataModel(helpers, model_name: str): metadataModel = MetadataModel( inputMModelLocation=helpers.get_data_path(model_name), inputMModelLocationType="local", @@ -55,20 +56,47 @@ class TestManifestValidation: @pytest.mark.parametrize( ("model_name", "manifest_name", "root_node"), [ - ("example.model.csv","mock_manifests/Valid_Test_Manifest.csv", "MockComponent"), - ("example.model.csv", "mock_manifests/Patient_test_no_entry_for_cond_required_column.manifest.csv", "Patient"), - ("example_test_nones.model.csv","mock_manifests/Valid_Test_Manifest_with_nones.csv", "MockComponent"), + ( + "example.model.csv", + "mock_manifests/Valid_Test_Manifest.csv", + "MockComponent", + ), + ( + "example.model.csv", + "mock_manifests/Patient_test_no_entry_for_cond_required_column.manifest.csv", + "Patient", + ), + ( + "example_test_nones.model.csv", + "mock_manifests/Valid_Test_Manifest_with_nones.csv", + "MockComponent", + ), + ], + ids=[ + "example_model", + "example_with_no_entry_for_cond_required_columns", + "example_with_nones", ], - ids=["example_model", "example_with_no_entry_for_cond_required_columns", "example_with_nones"], ) @pytest.mark.parametrize( "project_scope", ["syn54126707", "syn55250368", "syn55271234"], - ids=["project_scope_with_manifests", "project_scope_without_manifests", "project_scope_with_empty_manifest"], + ids=[ + "project_scope_with_manifests", + "project_scope_without_manifests", + "project_scope_with_empty_manifest", + ], ) - def test_valid_manifest(self, helpers, model_name:str, manifest_name:str, - root_node:str, project_scope:str, dmge:DataModelGraph): - """ Run the valid manifest in various situations, some of which will generate errors or warnings, + def test_valid_manifest( + self, + helpers, + model_name: str, + manifest_name: str, + root_node: str, + project_scope: str, + dmge: DataModelGraph, + ): + """Run the valid manifest in various situations, some of which will generate errors or warnings, if there are "issues" with target manifests on manifests. Since there are so many parameters, limit the combinations that are being run to the ones that are relevant. Args: @@ -90,16 +118,28 @@ def test_valid_manifest(self, helpers, model_name:str, manifest_name:str, manifest_path = helpers.get_data_path(manifest_name) warning_rule_sets_1 = [ - ('Check Match at Least', 'matchAtLeastOne Patient.PatientID set'), - ('Check Match at Least values', 'matchAtLeastOne MockComponent.checkMatchatLeastvalues value'), - ('Check Match Exactly', 'matchExactlyOne MockComponent.checkMatchExactly set'), - ('Check Match Exactly values', 'matchExactlyOne MockComponent.checkMatchExactlyvalues value'), - ] + ("Check Match at Least", "matchAtLeastOne Patient.PatientID set"), + ( + "Check Match at Least values", + "matchAtLeastOne MockComponent.checkMatchatLeastvalues value", + ), + ( + "Check Match Exactly", + "matchExactlyOne MockComponent.checkMatchExactly set", + ), + ( + "Check Match Exactly values", + "matchExactlyOne MockComponent.checkMatchExactlyvalues value", + ), + ] warning_rule_sets_2 = warning_rule_sets_1[1:] error_rule_sets = [ - ('Check Match None', 'matchNone MockComponent.checkMatchNone set error'), - ('Check Match None values', 'matchNone MockComponent.checkMatchNonevalues value error'), - ] + ("Check Match None", "matchNone MockComponent.checkMatchNone set error"), + ( + "Check Match None values", + "matchNone MockComponent.checkMatchNonevalues value error", + ), + ] # For the standard project scope, models and manifest should pass without warnings or errors if project_scope == "syn54126707": @@ -113,25 +153,34 @@ def test_valid_manifest(self, helpers, model_name:str, manifest_name:str, # When submitting the first manifest for cross manifest validation (MockComponent), check that proper warning # (to alert users that no validation will be run), is raised. The manifest is still valid to submit. - if (project_scope == "syn55250368" and root_node=="MockComponent" and - model_name in ["example.model.csv", "example_test_nones.model.csv"]): + if ( + project_scope == "syn55250368" + and root_node == "MockComponent" + and model_name in ["example.model.csv", "example_test_nones.model.csv"] + ): metadataModel = get_metadataModel(helpers, model_name) errors, warnings = metadataModel.validateModelManifest( manifestPath=manifest_path, rootNode=root_node, project_scope=[project_scope], ) - + for attribute_name, val_rule in warning_rule_sets_1: - assert GenerateError.generate_no_cross_warning( - dmge=dmge, - attribute_name=attribute_name, - val_rule=val_rule)[0] in warnings + assert ( + GenerateError.generate_no_cross_warning( + dmge=dmge, attribute_name=attribute_name, val_rule=val_rule + )[0] + in warnings + ) assert errors == [] - + # When submitting a manifest to a project that contains a manifest without data, ensure that the proper # warnings/errors are raised. - elif project_scope == "syn55271234" and root_node=="MockComponent" and model_name == "example.model.csv": + elif ( + project_scope == "syn55271234" + and root_node == "MockComponent" + and model_name == "example.model.csv" + ): metadataModel = get_metadataModel(helpers, model_name) errors, warnings = metadataModel.validateModelManifest( manifestPath=manifest_path, @@ -139,21 +188,24 @@ def test_valid_manifest(self, helpers, model_name:str, manifest_name:str, project_scope=[project_scope], ) for attribute_name, val_rule in warning_rule_sets_2: - assert GenerateError.generate_no_value_in_manifest_error( - dmge=dmge, - attribute_name=attribute_name, - val_rule=val_rule)[1][0] in warnings - - for attribute_name, val_rule in error_rule_sets: - assert GenerateError.generate_no_value_in_manifest_error( - dmge=dmge, - attribute_name=attribute_name, - val_rule=val_rule)[0][0] in errors + assert ( + GenerateError.generate_no_value_in_manifest_error( + dmge=dmge, attribute_name=attribute_name, val_rule=val_rule + )[1][0] + in warnings + ) + for attribute_name, val_rule in error_rule_sets: + assert ( + GenerateError.generate_no_value_in_manifest_error( + dmge=dmge, attribute_name=attribute_name, val_rule=val_rule + )[0][0] + in errors + ) def test_invalid_manifest(self, helpers, dmge): metadataModel = get_metadataModel(helpers, model_name="example.model.jsonld") - + manifestPath = helpers.get_data_path("mock_manifests/Invalid_Test_Manifest.csv") rootNode = "MockComponent" @@ -164,31 +216,41 @@ def test_invalid_manifest(self, helpers, dmge): ) # Check errors - assert GenerateError.generate_type_error( + assert ( + GenerateError.generate_type_error( val_rule="num", row_num="3", attribute_name="Check Num", invalid_entry="c", dmge=dmge, - )[0] in errors + )[0] + in errors + ) - assert GenerateError.generate_type_error( + assert ( + GenerateError.generate_type_error( val_rule="int", row_num="3", attribute_name="Check Int", invalid_entry="5.63", dmge=dmge, - )[0] in errors - - assert GenerateError.generate_type_error( + )[0] + in errors + ) + + assert ( + GenerateError.generate_type_error( val_rule="str", row_num="3", attribute_name="Check String", invalid_entry="94", dmge=dmge, - )[0] in errors + )[0] + in errors + ) - assert GenerateError.generate_list_error( + assert ( + GenerateError.generate_list_error( val_rule="list", list_string="9", row_num="3", @@ -196,9 +258,12 @@ def test_invalid_manifest(self, helpers, dmge): list_error="not_comma_delimited", invalid_entry="9", dmge=dmge, - )[0] in errors + )[0] + in errors + ) - assert GenerateError.generate_list_error( + assert ( + GenerateError.generate_list_error( val_rule="list", list_string="ab", row_num="4", @@ -206,9 +271,12 @@ def test_invalid_manifest(self, helpers, dmge): list_error="not_comma_delimited", invalid_entry="ab", dmge=dmge, - )[0] in errors + )[0] + in errors + ) - assert GenerateError.generate_list_error( + assert ( + GenerateError.generate_list_error( val_rule="list", list_string="a c f", row_num="3", @@ -216,9 +284,12 @@ def test_invalid_manifest(self, helpers, dmge): list_error="not_comma_delimited", invalid_entry="a c f", dmge=dmge, - )[0] in errors + )[0] + in errors + ) - assert GenerateError.generate_list_error( + assert ( + GenerateError.generate_list_error( val_rule="list", list_string="a", row_num="4", @@ -226,9 +297,12 @@ def test_invalid_manifest(self, helpers, dmge): list_error="not_comma_delimited", invalid_entry="a", dmge=dmge, - )[0] in errors + )[0] + in errors + ) - assert GenerateError.generate_list_error( + assert ( + GenerateError.generate_list_error( val_rule="list", list_string="a", row_num="4", @@ -236,9 +310,12 @@ def test_invalid_manifest(self, helpers, dmge): list_error="not_comma_delimited", invalid_entry="a", dmge=dmge, - )[0] in errors + )[0] + in errors + ) - assert GenerateError.generate_regex_error( + assert ( + GenerateError.generate_regex_error( val_rule="regex", reg_expression="[a-f]", row_num="3", @@ -246,9 +323,12 @@ def test_invalid_manifest(self, helpers, dmge): module_to_call="match", invalid_entry="m", dmge=dmge, - )[0] in errors + )[0] + in errors + ) - assert GenerateError.generate_regex_error( + assert ( + GenerateError.generate_regex_error( val_rule="regex", reg_expression="[a-f]", row_num="3", @@ -256,9 +336,12 @@ def test_invalid_manifest(self, helpers, dmge): module_to_call="search", invalid_entry="q", dmge=dmge, - )[0] in errors + )[0] + in errors + ) - assert GenerateError.generate_regex_error( + assert ( + GenerateError.generate_regex_error( val_rule="regex", reg_expression="^\d+$", row_num="2", @@ -266,9 +349,12 @@ def test_invalid_manifest(self, helpers, dmge): module_to_call="search", invalid_entry="5.4", dmge=dmge, - )[0] in errors + )[0] + in errors + ) - assert GenerateError.generate_url_error( + assert ( + GenerateError.generate_url_error( val_rule="url", url="http://googlef.com/", url_error="invalid_url", @@ -277,7 +363,9 @@ def test_invalid_manifest(self, helpers, dmge): argument=None, invalid_entry="http://googlef.com/", dmge=dmge, - )[0] in errors + )[0] + in errors + ) date_err = GenerateError.generate_content_error( val_rule="date", @@ -289,21 +377,27 @@ def test_invalid_manifest(self, helpers, dmge): error_in_list = [date_err[2] in error for error in errors] assert any(error_in_list) - assert GenerateError.generate_content_error( + assert ( + GenerateError.generate_content_error( val_rule="unique error", attribute_name="Check Unique", dmge=dmge, row_num=["2", "3", "4"], invalid_entry=["str1"], - )[0] in errors + )[0] + in errors + ) - assert GenerateError.generate_content_error( + assert ( + GenerateError.generate_content_error( val_rule="inRange 50 100 error", attribute_name="Check Range", dmge=dmge, row_num=["3"], invalid_entry=["30"], - )[0] in errors + )[0] + in errors + ) assert ( GenerateError.generate_cross_warning( @@ -314,7 +408,7 @@ def test_invalid_manifest(self, helpers, dmge): invalid_entry=["123"], dmge=dmge, )[0] - in errors + in errors ) assert ( @@ -325,54 +419,69 @@ def test_invalid_manifest(self, helpers, dmge): invalid_entry=["123"], dmge=dmge, )[0] - in errors + in errors ) # check warnings - assert GenerateError.generate_content_error( + assert ( + GenerateError.generate_content_error( val_rule="recommended", attribute_name="Check Recommended", dmge=dmge, - )[1] in warnings + )[1] + in warnings + ) - assert GenerateError.generate_content_error( + assert ( + GenerateError.generate_content_error( val_rule="protectAges", attribute_name="Check Ages", dmge=dmge, row_num=["2", "3"], invalid_entry=["6549", "32851"], - )[1] in warnings + )[1] + in warnings + ) - assert GenerateError.generate_cross_warning( + assert ( + GenerateError.generate_cross_warning( val_rule="matchAtLeastOne", row_num=["3"], attribute_name="Check Match at Least", invalid_entry=["7163"], manifest_id=["syn54126997", "syn54127001"], dmge=dmge, - )[1] in warnings + )[1] + in warnings + ) - assert GenerateError.generate_cross_warning( + assert ( + GenerateError.generate_cross_warning( val_rule="matchAtLeastOne MockComponent.checkMatchatLeastvalues value", row_num=["3"], attribute_name="Check Match at Least values", invalid_entry=["51100"], dmge=dmge, - )[1] in warnings + )[1] + in warnings + ) - assert \ + assert ( GenerateError.generate_cross_warning( val_rule="matchExactlyOne", attribute_name="Check Match Exactly", matching_manifests=["syn54126950", "syn54127008"], dmge=dmge, - )[1] in warnings \ + )[1] + in warnings or GenerateError.generate_cross_warning( val_rule="matchExactlyOne", attribute_name="Check Match Exactly", matching_manifests=["syn54127702", "syn54127008"], dmge=dmge, - )[1] in warnings + )[1] + in warnings + ) cross_warning = GenerateError.generate_cross_warning( val_rule="matchExactlyOne MockComponent.checkMatchExactlyvalues MockComponent.checkMatchExactlyvalues value", @@ -385,7 +494,6 @@ def test_invalid_manifest(self, helpers, dmge): warning_in_list = [cross_warning[1] in warning for warning in warnings] assert any(warning_in_list) - def test_in_house_validation(self, helpers, dmge): metadataModel = get_metadataModel(helpers, model_name="example.model.jsonld") manifestPath = helpers.get_data_path("mock_manifests/Invalid_Test_Manifest.csv") @@ -399,39 +507,52 @@ def test_in_house_validation(self, helpers, dmge): ) # Check errors - assert GenerateError.generate_type_error( + assert ( + GenerateError.generate_type_error( val_rule="num", row_num="3", attribute_name="Check Num", invalid_entry="c", dmge=dmge, - )[0] in errors + )[0] + in errors + ) - assert GenerateError.generate_type_error( + assert ( + GenerateError.generate_type_error( val_rule="int", row_num="3", attribute_name="Check Int", invalid_entry="5.63", dmge=dmge, - )[0] in errors + )[0] + in errors + ) - assert GenerateError.generate_type_error( + assert ( + GenerateError.generate_type_error( val_rule="str", row_num="3", attribute_name="Check String", invalid_entry="94", dmge=dmge, - )[0] in errors + )[0] + in errors + ) - assert GenerateError.generate_type_error( + assert ( + GenerateError.generate_type_error( val_rule="int", row_num="3", attribute_name="Check NA", invalid_entry="9.5", dmge=dmge, - )[0] in errors + )[0] + in errors + ) - assert GenerateError.generate_list_error( + assert ( + GenerateError.generate_list_error( val_rule="list", list_string="9", row_num="3", @@ -439,9 +560,12 @@ def test_in_house_validation(self, helpers, dmge): list_error="not_comma_delimited", invalid_entry="9", dmge=dmge, - )[0] in errors + )[0] + in errors + ) - assert GenerateError.generate_list_error( + assert ( + GenerateError.generate_list_error( val_rule="list", list_string="ab", row_num="4", @@ -449,9 +573,12 @@ def test_in_house_validation(self, helpers, dmge): list_error="not_comma_delimited", invalid_entry="ab", dmge=dmge, - )[0] in errors + )[0] + in errors + ) - assert GenerateError.generate_regex_error( + assert ( + GenerateError.generate_regex_error( val_rule="regex", reg_expression="[a-f]", row_num="3", @@ -459,9 +586,12 @@ def test_in_house_validation(self, helpers, dmge): module_to_call="search", invalid_entry="q", dmge=dmge, - )[0] in errors + )[0] + in errors + ) - assert GenerateError.generate_regex_error( + assert ( + GenerateError.generate_regex_error( val_rule="regex", reg_expression="[a-f]", row_num="3", @@ -469,9 +599,12 @@ def test_in_house_validation(self, helpers, dmge): module_to_call="match", invalid_entry="m", dmge=dmge, - )[0] in errors + )[0] + in errors + ) - assert GenerateError.generate_url_error( + assert ( + GenerateError.generate_url_error( val_rule="url", url="http://googlef.com/", url_error="invalid_url", @@ -480,7 +613,9 @@ def test_in_house_validation(self, helpers, dmge): argument=None, invalid_entry="http://googlef.com/", dmge=dmge, - )[0] in errors + )[0] + in errors + ) assert ( GenerateError.generate_cross_warning( @@ -491,7 +626,7 @@ def test_in_house_validation(self, helpers, dmge): invalid_entry=["123"], dmge=dmge, )[0] - in errors + in errors ) assert ( @@ -502,56 +637,66 @@ def test_in_house_validation(self, helpers, dmge): invalid_entry=["123"], dmge=dmge, )[0] - in errors + in errors ) # Check Warnings - assert GenerateError.generate_cross_warning( + assert ( + GenerateError.generate_cross_warning( val_rule="matchAtLeastOne", row_num=["3"], attribute_name="Check Match at Least", invalid_entry=["7163"], manifest_id=["syn54126997", "syn54127001"], dmge=dmge, - )[1] in warnings + )[1] + in warnings + ) - assert GenerateError.generate_cross_warning( + assert ( + GenerateError.generate_cross_warning( val_rule="matchAtLeastOne MockComponent.checkMatchatLeastvalues value", row_num=["3"], attribute_name="Check Match at Least values", invalid_entry=["51100"], dmge=dmge, - )[1] in warnings + )[1] + in warnings + ) - assert \ + assert ( GenerateError.generate_cross_warning( val_rule="matchExactlyOne", attribute_name="Check Match Exactly", matching_manifests=["syn54126950", "syn54127008"], dmge=dmge, - )[1] in warnings \ + )[1] + in warnings or GenerateError.generate_cross_warning( val_rule="matchExactlyOne", attribute_name="Check Match Exactly", matching_manifests=["syn54127702", "syn54127008"], dmge=dmge, - )[1] in warnings + )[1] + in warnings + ) - assert GenerateError.generate_cross_warning( + assert ( + GenerateError.generate_cross_warning( val_rule="matchExactlyOne MockComponent.checkMatchExactlyvalues MockComponent.checkMatchExactlyvalues value", row_num=["2", "3", "4"], attribute_name="Check Match Exactly values", invalid_entry=["71738", "98085", "210065"], dmge=dmge, - )[1] in warnings - + )[1] + in warnings + ) - def test_missing_column(self, helpers, dmge:DataModelGraph): - """ Test that a manifest missing a column returns the proper error. - """ - model_name="example.model.csv" - manifest_name="mock_manifests/Invalid_Biospecimen_Missing_Column_Manifest.csv" - root_node="Biospecimen" + def test_missing_column(self, helpers, dmge: DataModelGraph): + """Test that a manifest missing a column returns the proper error.""" + model_name = "example.model.csv" + manifest_name = "mock_manifests/Invalid_Biospecimen_Missing_Column_Manifest.csv" + root_node = "Biospecimen" manifest_path = helpers.get_data_path(manifest_name) metadataModel = get_metadataModel(helpers, model_name) @@ -560,14 +705,16 @@ def test_missing_column(self, helpers, dmge:DataModelGraph): rootNode=root_node, ) - assert GenerateError.generate_schema_error( - row_num='2', + assert ( + GenerateError.generate_schema_error( + row_num="2", attribute_name="Wrong schema", error_message="'Tissue Status' is a required property", invalid_entry="Wrong schema", dmge=dmge, - )[0] in errors - + )[0] + in errors + ) @pytest.mark.parametrize( "model_name", @@ -577,19 +724,46 @@ def test_missing_column(self, helpers, dmge:DataModelGraph): ], ids=["example_model", "example_with_requirements_from_vr"], ) - @pytest.mark.parametrize( - ["manifest_name", "root_node",], [ - ("mock_manifests/Biospecimen_required_vr_test_fail.manifest.csv", "Biospecimen"), - ("mock_manifests/Biospecimen_required_vr_test_pass.manifest.csv", "Biospecimen"), + "manifest_name", + "root_node", + ], + [ + ( + "mock_manifests/Biospecimen_required_vr_test_fail.manifest.csv", + "Biospecimen", + ), + ( + "mock_manifests/Biospecimen_required_vr_test_pass.manifest.csv", + "Biospecimen", + ), ("mock_manifests/Patient_required_vr_test_pass.manifest.csv", "Patient"), - ("mock_manifests/Patient_test_no_entry_for_cond_required_column.manifest.csv", "Patient"), - ("mock_manifests/BulkRNAseq_component_based_required_rule_test.manifest.csv", "BulkRNA-seqAssay"), + ( + "mock_manifests/Patient_test_no_entry_for_cond_required_column.manifest.csv", + "Patient", + ), + ( + "mock_manifests/BulkRNAseq_component_based_required_rule_test.manifest.csv", + "BulkRNA-seqAssay", + ), + ], + ids=[ + "biospeciment_required_vr_empty", + "biospecimen_required_filled", + "patient_not_required_empty", + "patient_conditionally_required_not_filled", + "bulk_rna_seq_component_based_rule_test", ], - ids=["biospeciment_required_vr_empty", "biospecimen_required_filled", "patient_not_required_empty", "patient_conditionally_required_not_filled", "bulk_rna_seq_component_based_rule_test"], ) - def test_required_validation_rule(self, helpers, model_name:str, manifest_name:str, root_node:str, dmge:DataModelGraphExplorer) -> None: + def test_required_validation_rule( + self, + helpers, + model_name: str, + manifest_name: str, + root_node: str, + dmge: DataModelGraphExplorer, + ) -> None: """ Args: model_name, str: model to run test validation against @@ -630,7 +804,11 @@ def test_required_validation_rule(self, helpers, model_name:str, manifest_name:s rootNode=root_node, ) - error_and_warning_free_manifests = ["Biospecimen_required_vr_test_pass", "Patient_test_no_entry_for_cond_required_column", ""] + error_and_warning_free_manifests = [ + "Biospecimen_required_vr_test_pass", + "Patient_test_no_entry_for_cond_required_column", + "", + ] # For each model, these manifest should pass, bc either the value is being passed as requierd, or its not currently required for manifest in error_and_warning_free_manifests: @@ -638,70 +816,85 @@ def test_required_validation_rule(self, helpers, model_name:str, manifest_name:s assert errors == [] assert warnings == [] - messages = {"patient_id_empty_warning": { - "row_num":"2", - "attribute_name":"Patient ID", - "error_message":"'' should be non-empty", - "invalid_entry":""}, - "bulk_rnaseq_cbr_error_1":{ - "row_num":"3", - "attribute_name":"Genome FASTA", - "error_message":"'' should be non-empty", - "invalid_entry":""}, - "bulk_rnaseq_cbr_error_2":{ - "row_num":"4", - "attribute_name":"File Format", - "error_message":"'' is not one of ['CSV/TSV', 'CRAM', 'FASTQ', 'BAM']", - "invalid_entry":""}, - } + messages = { + "patient_id_empty_warning": { + "row_num": "2", + "attribute_name": "Patient ID", + "error_message": "'' should be non-empty", + "invalid_entry": "", + }, + "bulk_rnaseq_cbr_error_1": { + "row_num": "3", + "attribute_name": "Genome FASTA", + "error_message": "'' should be non-empty", + "invalid_entry": "", + }, + "bulk_rnaseq_cbr_error_2": { + "row_num": "4", + "attribute_name": "File Format", + "error_message": "'' is not one of ['CSV/TSV', 'CRAM', 'FASTQ', 'BAM']", + "invalid_entry": "", + }, + } # This manifest should fail in the example_model bc the manifest Required=False, and in the example_with_requirements_from_vr # bc the requirments are set to false in the validation rule - if (("Biospecimen_required_vr_test_fail" in manifest_name) or - ("Patient_required_vr_test_pass" in manifest_name and model_name == "example.model.csv") - ): + if ("Biospecimen_required_vr_test_fail" in manifest_name) or ( + "Patient_required_vr_test_pass" in manifest_name + and model_name == "example.model.csv" + ): message_key = "patient_id_empty_warning" - assert GenerateError.generate_schema_error( - row_num=messages[message_key]["row_num"], - attribute_name=messages[message_key]["attribute_name"], - error_message=messages[message_key]["error_message"], - invalid_entry=messages[message_key]["invalid_entry"], - dmge=dmge, - )[0] in errors + assert ( + GenerateError.generate_schema_error( + row_num=messages[message_key]["row_num"], + attribute_name=messages[message_key]["attribute_name"], + error_message=messages[message_key]["error_message"], + invalid_entry=messages[message_key]["invalid_entry"], + dmge=dmge, + )[0] + in errors + ) assert warnings == [] - if "Patient_required_vr_test_pass" in manifest_name and model_name == "example_required_vr_test.model.csv": + if ( + "Patient_required_vr_test_pass" in manifest_name + and model_name == "example_required_vr_test.model.csv" + ): assert errors == [] assert warnings == [] if "BulkRNAseq_component_based_required_rule_test" in manifest_name: message_key = "bulk_rnaseq_cbr_error_1" - assert GenerateError.generate_schema_error( + assert ( + GenerateError.generate_schema_error( row_num=messages[message_key]["row_num"], attribute_name=messages[message_key]["attribute_name"], error_message=messages[message_key]["error_message"], invalid_entry=messages[message_key]["invalid_entry"], dmge=dmge, - )[0] in errors + )[0] + in errors + ) message_key = "bulk_rnaseq_cbr_error_2" expected_error = GenerateError.generate_schema_error( - row_num=messages[message_key]["row_num"], - attribute_name=messages[message_key]["attribute_name"], - error_message=messages[message_key]["error_message"], - invalid_entry=messages[message_key]["invalid_entry"], - dmge=dmge, - )[0] + row_num=messages[message_key]["row_num"], + attribute_name=messages[message_key]["attribute_name"], + error_message=messages[message_key]["error_message"], + invalid_entry=messages[message_key]["invalid_entry"], + dmge=dmge, + )[0] # since the valid value order isnt set in error reporting, check a portion of the expected output # Check the error row is expected assert expected_error[1] in errors[1] # Check that one of the values for the expected valid values is present # Extract a valid value - valid_value = expected_error[2].split(',')[-1].split(']')[0].strip(' ').strip("\'") - assert valid_value in errors[1][2] - assert warnings==[] - + valid_value = ( + expected_error[2].split(",")[-1].split("]")[0].strip(" ").strip("'") + ) + assert valid_value in errors[1][2] + assert warnings == [] @pytest.mark.parametrize( "manifest_path", @@ -756,13 +949,16 @@ def test_component_validations(self, helpers, manifest_path, dmge): and vmr_warnings[0][-1] == ["123"] ) - @pytest.mark.rule_combos( reason="This introduces a great number of tests covering every possible rule combination that are only necessary on occasion." ) @pytest.mark.parametrize("base_rule, second_rule", get_rule_combinations()) def test_rule_combinations( - self, helpers, dmge, base_rule, second_rule, + self, + helpers, + dmge, + base_rule, + second_rule, ): """ TODO: Describe what this test is doing.