From 930fbd6152ed31c1b3eff654e4e7fe7fc72475ab Mon Sep 17 00:00:00 2001 From: Mialy DeFelice <85905780+mialy-defelice@users.noreply.github.com> Date: Wed, 17 Jan 2024 06:38:52 -0800 Subject: [PATCH] Revert "Refactor Schemas: JSONLD Data Model Parsing, change from using labels to display names, merge develop" --- .github/workflows/test.yml | 6 +- great_expectations/great_expectations.yml | 109 +++ poetry.lock | 1035 +++++++++------------ pyproject.toml | 4 +- schematic/manifest/commands.py | 16 +- schematic/manifest/generator.py | 131 +-- schematic/models/GE_Helpers.py | 13 +- schematic/models/metadata.py | 28 +- schematic/models/validate_manifest.py | 1 - schematic/schemas/data_model_nodes.py | 3 +- schematic/schemas/data_model_parser.py | 42 +- schematic/store/synapse.py | 27 +- schematic/utils/validate_utils.py | 20 +- schematic/visualization/tangled_tree.py | 4 +- schematic_api/api/routes.py | 85 +- tests/conftest.py | 12 - tests/data/example.model.jsonld | 34 +- tests/test_api.py | 11 +- tests/test_cli.py | 6 +- tests/test_manifest.py | 20 +- tests/test_schemas.py | 13 +- tests/test_store.py | 68 +- tests/test_utils.py | 13 +- tests/test_validation.py | 13 +- 24 files changed, 816 insertions(+), 898 deletions(-) create mode 100644 great_expectations/great_expectations.yml diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml index 809c350d4..720dcfcae 100644 --- a/.github/workflows/test.yml +++ b/.github/workflows/test.yml @@ -25,7 +25,7 @@ concurrency: cancel-in-progress: true jobs: test: - runs-on: ubuntu-22.04-4core-16GBRAM-150GBSSD + runs-on: ubuntu-latest env: POETRY_VERSION: 1.3.0 strategy: @@ -128,7 +128,7 @@ jobs: run: > source .venv/bin/activate; pytest --durations=0 --cov-report=term --cov-report=html:htmlcov --cov=schematic/ - -m "not (google_credentials_needed or schematic_api or table_operations)" --reruns 2 -n auto + -m "not (google_credentials_needed or schematic_api or table_operations)" - name: Run tests env: @@ -138,7 +138,7 @@ jobs: run: > source .venv/bin/activate; pytest --durations=0 --cov-report=term --cov-report=html:htmlcov --cov=schematic/ - -m "not (google_credentials_needed or rule_combos or schematic_api or table_operations)" --reruns 2 -n auto + -m "not (google_credentials_needed or rule_combos or schematic_api or table_operations)" - name: Upload pytest test results uses: actions/upload-artifact@v2 diff --git a/great_expectations/great_expectations.yml b/great_expectations/great_expectations.yml new file mode 100644 index 000000000..60b73a8f3 --- /dev/null +++ b/great_expectations/great_expectations.yml @@ -0,0 +1,109 @@ +# Welcome to Great Expectations! Always know what to expect from your data. +# +# Here you can define datasources, batch kwargs generators, integrations and +# more. This file is intended to be committed to your repo. For help with +# configuration please: +# - Read our docs: https://docs.greatexpectations.io/en/latest/reference/spare_parts/data_context_reference.html#configuration +# - Join our slack channel: http://greatexpectations.io/slack + +# config_version refers to the syntactic version of this config file, and is used in maintaining backwards compatibility +# It is auto-generated and usually does not need to be changed. +config_version: 3.0 + +# Datasources tell Great Expectations where your data lives and how to get it. +# You can use the CLI command `great_expectations datasource new` to help you +# add a new datasource. Read more at https://docs.greatexpectations.io/en/latest/reference/core_concepts/datasource.html +datasources: + Manifest: + module_name: great_expectations.datasource + execution_engine: + module_name: great_expectations.execution_engine + class_name: PandasExecutionEngine + data_connectors: + default_runtime_data_connector_name: + module_name: great_expectations.datasource.data_connector + class_name: RuntimeDataConnector + batch_identifiers: + - default_identifier + class_name: Datasource + example_datasource: + module_name: great_expectations.datasource + execution_engine: + module_name: great_expectations.execution_engine + class_name: PandasExecutionEngine + data_connectors: + default_runtime_data_connector_name: + module_name: great_expectations.datasource.data_connector + class_name: RuntimeDataConnector + batch_identifiers: + - default_identifier_name + class_name: Datasource +config_variables_file_path: uncommitted/config_variables.yml + +# The plugins_directory will be added to your python path for custom modules +# used to override and extend Great Expectations. +plugins_directory: plugins/ + +stores: +# Stores are configurable places to store things like Expectations, Validations +# Data Docs, and more. These are for advanced users only - most users can simply +# leave this section alone. +# +# Three stores are required: expectations, validations, and +# evaluation_parameters, and must exist with a valid store entry. Additional +# stores can be configured for uses such as data_docs, etc. + expectations_store: + class_name: ExpectationsStore + store_backend: + class_name: TupleFilesystemStoreBackend + base_directory: expectations/ + + validations_store: + class_name: ValidationsStore + store_backend: + class_name: TupleFilesystemStoreBackend + base_directory: uncommitted/validations/ + + evaluation_parameter_store: + # Evaluation Parameters enable dynamic expectations. Read more here: + # https://docs.greatexpectations.io/en/latest/reference/core_concepts/evaluation_parameters.html + class_name: EvaluationParameterStore + + checkpoint_store: + class_name: CheckpointStore + store_backend: + class_name: TupleFilesystemStoreBackend + suppress_store_backend_id: true + base_directory: checkpoints/ + + profiler_store: + class_name: ProfilerStore + store_backend: + class_name: TupleFilesystemStoreBackend + suppress_store_backend_id: true + base_directory: profilers/ + +expectations_store_name: expectations_store +validations_store_name: validations_store +evaluation_parameter_store_name: evaluation_parameter_store +checkpoint_store_name: checkpoint_store + +data_docs_sites: + # Data Docs make it simple to visualize data quality in your project. These + # include Expectations, Validations & Profiles. The are built for all + # Datasources from JSON artifacts in the local repo including validations & + # profiles from the uncommitted directory. Read more at https://docs.greatexpectations.io/en/latest/reference/core_concepts/data_docs.html + local_site: + class_name: SiteBuilder + # set to false to hide how-to buttons in Data Docs + show_how_to_buttons: true + store_backend: + class_name: TupleFilesystemStoreBackend + base_directory: uncommitted/data_docs/local_site/ + site_index_builder: + class_name: DefaultSiteIndexBuilder + +anonymous_usage_statistics: + data_context_id: 1130ca8d-9731-45d9-bc05-2032535250c8 + enabled: true +notebooks: diff --git a/poetry.lock b/poetry.lock index 746ce0027..aa335ffa3 100644 --- a/poetry.lock +++ b/poetry.lock @@ -1,4 +1,4 @@ -# This file is automatically @generated by Poetry 1.7.1 and should not be changed by hand. +# This file is automatically @generated by Poetry and should not be changed by hand. 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("manifest", "get", "data_type")), ) @click.option( - "-p", "--path_to_data_model", help=query_dict(manifest_commands, ("manifest", "get", "path_to_data_model")) + "-p", "--jsonld", help=query_dict(manifest_commands, ("manifest", "get", "jsonld")) ) @click.option( "-d", @@ -107,7 +107,7 @@ def get_manifest( ctx, title, data_type, - path_to_data_model, + jsonld, dataset_id, sheet_url, output_csv, @@ -124,14 +124,14 @@ def get_manifest( if data_type is None: data_type = CONFIG.manifest_data_type log_value_from_config("data_type", data_type) - if path_to_data_model is None: - path_to_data_model = CONFIG.model_location - log_value_from_config("path_to_data_model", path_to_data_model) + if jsonld is None: + jsonld = CONFIG.model_location + log_value_from_config("jsonld", jsonld) if title is None: title = CONFIG.manifest_title log_value_from_config("title", title) - data_model_parser = DataModelParser(path_to_data_model = path_to_data_model) + data_model_parser = DataModelParser(path_to_data_model = jsonld) #Parse Model logger.info("Parsing data model.") @@ -147,7 +147,7 @@ def get_manifest( def create_single_manifest(data_type, output_csv=None, output_xlsx=None): # create object of type ManifestGenerator manifest_generator = ManifestGenerator( - path_to_data_model=path_to_data_model, + path_to_json_ld=jsonld, graph = graph_data_model, title=t, root=data_type, @@ -191,7 +191,7 @@ def create_single_manifest(data_type, output_csv=None, output_xlsx=None): logger.info("Find the manifest template using this Google Sheet URL:") click.echo(result) if output_csv is None and output_xlsx is None: - prefix, _ = os.path.splitext(path_to_data_model) + prefix, _ = os.path.splitext(jsonld) prefix_root, prefix_ext = os.path.splitext(prefix) if prefix_ext == ".model": prefix = prefix_root diff --git a/schematic/manifest/generator.py b/schematic/manifest/generator.py index 049941ff2..9d6f6e997 100644 --- a/schematic/manifest/generator.py +++ b/schematic/manifest/generator.py @@ -10,13 +10,10 @@ from pathlib import Path import pygsheets as ps from tempfile import NamedTemporaryFile -from typing import Dict, List, Optional, Tuple, Union, BinaryIO, Literal -from flask import send_from_directory +from typing import Dict, List, Optional, Tuple, Union -from schematic.schemas.data_model_graph import DataModelGraph, DataModelGraphExplorer -from schematic.schemas.data_model_parser import DataModelParser +from schematic.schemas.data_model_graph import DataModelGraphExplorer from schematic.schemas.data_model_json_schema import DataModelJSONSchema - from schematic.utils.google_api_utils import ( execute_google_api_requests, build_service_account_creds, @@ -39,7 +36,7 @@ class ManifestGenerator(object): def __init__( self, - path_to_data_model: str, # JSON-LD file to be used for generating the manifest + path_to_json_ld: str, # JSON-LD file to be used for generating the manifest graph: nx.MultiDiGraph, # At this point, the graph is fully formed. alphabetize_valid_values: str = 'ascending', title: str = None, # manifest sheet title @@ -60,7 +57,7 @@ def __init__( self.creds = services_creds["creds"] # Path to jsonld - self.model_path = path_to_data_model + self.jsonld_path = path_to_json_ld # Graph self.graph = graph @@ -378,7 +375,7 @@ def _get_json_schema(self, json_schema_filepath: str) -> Dict: """ if not json_schema_filepath: # TODO Catch error if no JSONLD or JSON path provided. - data_model_js = DataModelJSONSchema(jsonld_path=self.model_path, graph=self.graph) + data_model_js = DataModelJSONSchema(jsonld_path=self.jsonld_path, graph=self.graph) json_schema = data_model_js.get_json_validation_schema(source_node=self.root, schema_name=self.title) else: with open(json_schema_filepath) as jsonfile: @@ -1318,7 +1315,7 @@ def set_dataframe_by_url( sh = gc.open_by_url(manifest_url) wb = sh[0] - wb.set_dataframe(manifest_df, (1, 1), fit=True) + wb.set_dataframe(manifest_df, (1, 1)) # update validation rules (i.e. no validation rules) for out of schema columns, if any # TODO: similarly clear formatting for out of schema columns, if any @@ -1498,121 +1495,6 @@ def _handle_output_format_logic(self, output_format: str = None, output_path: st # Default return a DataFrame else: return dataframe - - @staticmethod - def create_single_manifest(path_to_data_model: str, graph_data_model: nx.MultiDiGraph, data_type: str, access_token:Optional[str]=None, dataset_id:Optional[str]=None, strict:Optional[bool]=True, title:Optional[str]=None, output_format:Literal["google_sheet", "excel", "dataframe"]="google_sheet", use_annotations:Optional[bool]=False) -> Union[str, pd.DataFrame, BinaryIO]: - """Create a single manifest - - Args: - jsonld (str): jsonld schema - data_type (str): data type of a manifest - access_token (str, optional): synapse access token. Required when getting an existing manifest. Defaults to None. - dataset_id (str, optional): dataset id when generating an existing manifest. Defaults to None. - strict (bool, optional): strictness with which to apply validation rules to google sheets. Defaults to True. - title (str, optional): title of a given manifest. Defaults to None. - output_format (str, optional): format of manifest. It has three options: google sheet, excel or dataframe. Defaults to None. - use_annotations (bool, optional): whether to use annotations. Defaults to False. - - Returns: - Union[str, pd.DataFrame, BinaryIO]: Googlesheet URL or pandas dataframe or Excel. - """ - # create object of type ManifestGenerator - manifest_generator = ManifestGenerator( - path_to_data_model=path_to_data_model, - graph=graph_data_model, - title=title, - root=data_type, - use_annotations=use_annotations, - alphabetize_valid_values = 'ascending', - ) - - # if returning a dataframe - if output_format: - if "dataframe" in output_format: - output_format = "dataframe" - - result = manifest_generator.get_manifest( - dataset_id=dataset_id, sheet_url=True, output_format=output_format, access_token=access_token, strict=strict, - ) - - # return an excel file if output_format is set to "excel" - if output_format == "excel": - dir_name = os.path.dirname(result) - file_name = os.path.basename(result) - mimetype='application/vnd.openxmlformats-officedocument.spreadsheetml.sheet' - return send_from_directory(directory=dir_name, path=file_name, as_attachment=True, mimetype=mimetype, max_age=0) - - return result - - @staticmethod - def create_manifests(path_to_data_model:str, data_types:list, access_token:Optional[str]=None, dataset_ids:Optional[list]=None, output_format:Literal["google_sheet", "excel", "dataframe"]="google_sheet", title:Optional[str]=None, strict:Optional[bool]=True, use_annotations:Optional[bool]=False) -> Union[List[str], List[pd.DataFrame], BinaryIO]: - """Create multiple manifests - - Args: - path_to_data_model (str): str path to data model - data_type (list): a list of data types - access_token (str, optional): synapse access token. Required when getting an existing manifest. Defaults to None. - dataset_id (list, optional): a list of dataset ids when generating an existing manifest. Defaults to None. - output_format (str, optional):format of manifest. It has three options: google sheet, excel or dataframe. Defaults to None. - title (str, optional): title of a given manifest. Defaults to None. - strict (bool, optional): strictness with which to apply validation rules to google sheets. Defaults to None. - use_annotations (bool, optional): whether to use annotations. Defaults to False. - - Returns: - Union[List[str], List[pd.DataFrame], BinaryIO]: a list of Googlesheet URLs, a list of pandas dataframes or an Excel file. - """ - data_model_parser = DataModelParser(path_to_data_model = path_to_data_model) - - #Parse Model - parsed_data_model = data_model_parser.parse_model() - - # Instantiate DataModelGraph - data_model_grapher = DataModelGraph(parsed_data_model) - - # Generate graph - graph_data_model = data_model_grapher.generate_data_model_graph() - - # Gather all returned result urls - all_results = [] - if data_types[0] == 'all manifests': - dmge = DataModelGraphExplorer(graph_data_model) - component_digraph = dmge.get_digraph_by_edge_type('requiresComponent') - components = component_digraph.nodes() - for component in components: - if title: - t = f'{title}.{component}.manifest' - else: - t = f'Example.{component}.manifest' - if output_format != "excel": - result = ManifestGenerator.create_single_manifest(path_to_data_model=path_to_data_model, data_type=component, graph_data_model=graph_data_model, output_format=output_format, title=t, access_token=access_token) - all_results.append(result) - else: - logger.error('Currently we do not support returning multiple files as Excel format at once. Please choose a different output format. ') - else: - for i, dt in enumerate(data_types): - if not title: - t = f'Example.{dt}.manifest' - else: - if len(data_types) > 1: - t = f'{title}.{dt}.manifest' - else: - t = title - if dataset_ids: - # if a dataset_id is provided add this to the function call. - result = ManifestGenerator.create_single_manifest(path_to_data_model=path_to_data_model, data_type=dt, graph_data_model=graph_data_model, dataset_id=dataset_ids[i], output_format=output_format, title=t, access_token=access_token, use_annotations=use_annotations) - else: - result = ManifestGenerator.create_single_manifest(path_to_data_model=path_to_data_model, data_type=dt, graph_data_model=graph_data_model, output_format=output_format, title=t, access_token=access_token, use_annotations=use_annotations) - - # if output is pandas dataframe or google sheet url - if isinstance(result, str) or isinstance(result, pd.DataFrame): - all_results.append(result) - else: - if len(data_types) > 1: - logger.warning(f'Currently we do not support returning multiple files as Excel format at once. Only {t} would get returned. ') - return result - - return all_results - def get_manifest( self, dataset_id: str = None, sheet_url: bool = None, json_schema: str = None, output_format: str = None, output_path: str = None, access_token: str = None, strict: Optional[bool]=None, @@ -1630,6 +1512,7 @@ def get_manifest( Returns: Googlesheet URL, pandas dataframe, or an Excel spreadsheet """ + # Handle case when no dataset ID is provided if not dataset_id: manifest_url = self.get_empty_manifest(json_schema_filepath=json_schema, strict=strict, sheet_url=sheet_url) diff --git a/schematic/models/GE_Helpers.py b/schematic/models/GE_Helpers.py index 521d75157..f183d1daa 100644 --- a/schematic/models/GE_Helpers.py +++ b/schematic/models/GE_Helpers.py @@ -146,9 +146,10 @@ def build_expectation_suite(self,): } #create blank expectation suite - self.expectation_suite_name = "Manifest_test_suite" - self.suite = self.context.add_expectation_suite( - expectation_suite_name=self.expectation_suite_name, + expectation_suite_name = "Manifest_test_suite" + self.suite = self.context.create_expectation_suite( + expectation_suite_name=expectation_suite_name, + overwrite_existing=True ) #build expectation configurations for each expectation @@ -307,9 +308,9 @@ def build_expectation_suite(self,): ) - self.context.update_expectation_suite(expectation_suite=self.suite,) + self.context.save_expectation_suite(expectation_suite=self.suite, expectation_suite_name=expectation_suite_name) - suite_identifier = ExpectationSuiteIdentifier(expectation_suite_name=self.expectation_suite_name) + suite_identifier = ExpectationSuiteIdentifier(expectation_suite_name=expectation_suite_name) self.context.build_data_docs(resource_identifiers=[suite_identifier]) ##Webpage DataDocs opened here: #self.context.open_data_docs(resource_identifier=suite_identifier) @@ -370,7 +371,7 @@ def build_checkpoint(self): "data_connector_name": "default_runtime_data_connector_name", "data_asset_name": "Manifest", }, - "expectation_suite_name": self.expectation_suite_name, + "expectation_suite_name": "Manifest_test_suite", } ], } diff --git a/schematic/models/metadata.py b/schematic/models/metadata.py index 50e718014..1d86fb00a 100644 --- a/schematic/models/metadata.py +++ b/schematic/models/metadata.py @@ -1,7 +1,7 @@ -import os import logging import networkx as nx from jsonschema import ValidationError +from os.path import exists # allows specifying explicit variable types from typing import Any, Dict, Optional, Text, List @@ -185,14 +185,8 @@ def get_component_requirements( # TODO: abstract validation in its own module def validateModelManifest( - self, - manifestPath: str, - rootNode: str, - restrict_rules: bool = False, - jsonSchema: Optional[str] = None, - project_scope: Optional[List] = None, - access_token: Optional[str] = None, - ) -> tuple[list, list]: + self, manifestPath: str, rootNode: str, restrict_rules: bool = False, jsonSchema: str = None, project_scope: List = None, access_token: str = None, + ) -> List[str]: """Check if provided annotations manifest dataframe satisfies all model requirements. Args: @@ -259,11 +253,7 @@ def validateModelManifest( ) return errors, warnings - - # check if suite has been created. If so, delete it - if os.path.exists("great_expectations/expectations/Manifest_test_suite.json"): - os.remove("great_expectations/expectations/Manifest_test_suite.json") - + errors, warnings, manifest = validate_all(self, errors=errors, warnings=warnings, @@ -291,7 +281,7 @@ def populateModelManifest(self, title, manifestPath: str, rootNode: str, return_ ValueError: rootNode not found in metadata model. """ mg = ManifestGenerator( - path_to_data_model=self.inputMModelLocation, graph = self.graph_data_model, title=title, root=rootNode + path_to_json_ld=self.inputMModelLocation, graph = self.graph_data_model, title=title, root=rootNode ) emptyManifestURL = mg.get_manifest() @@ -305,10 +295,10 @@ def submit_metadata_manifest( dataset_id: str, manifest_record_type: str, restrict_rules: bool, - access_token: Optional[str] = None, - validate_component: Optional[str] = None, + validate_component: str = None, use_schema_label: bool = True, hide_blanks: bool = False, + access_token: str = None, project_scope: List = None, table_manipulation: str = 'replace' ) -> str: @@ -356,7 +346,7 @@ def submit_metadata_manifest( # if there are no errors in validation process if val_errors == []: # upload manifest file from `manifest_path` path to entity with Syn ID `dataset_id` - if os.path.exists(censored_manifest_path): + if exists(censored_manifest_path): censored_manifest_id = syn_store.associateMetadataWithFiles( dmge = self.dmge, metadataManifestPath = censored_manifest_path, @@ -389,7 +379,7 @@ def submit_metadata_manifest( ) # no need to perform validation, just submit/associate the metadata manifest file - if os.path.exists(censored_manifest_path): + if exists(censored_manifest_path): censored_manifest_id = syn_store.associateMetadataWithFiles( dmge = self.dmge, metadataManifestPath=censored_manifest_path, diff --git a/schematic/models/validate_manifest.py b/schematic/models/validate_manifest.py index ff180998a..702c700b0 100644 --- a/schematic/models/validate_manifest.py +++ b/schematic/models/validate_manifest.py @@ -153,7 +153,6 @@ def validate_manifest_rules( ) finally: ge_helpers.context.delete_checkpoint(ge_helpers.checkpoint_name) - ge_helpers.context.delete_expectation_suite(ge_helpers.expectation_suite_name) validation_results = results.list_validation_results() diff --git a/schematic/schemas/data_model_nodes.py b/schematic/schemas/data_model_nodes.py index e82369789..a1681c469 100644 --- a/schematic/schemas/data_model_nodes.py +++ b/schematic/schemas/data_model_nodes.py @@ -3,7 +3,6 @@ from rdflib import Namespace from typing import Any, Dict, Optional, Text, List, Callable -from schematic.schemas.data_model_parser import DataModelJSONLDParser from schematic.schemas.data_model_relationships import DataModelRelationships from schematic.utils.schema_utils import ( @@ -53,7 +52,7 @@ def gather_nodes(self, attr_info: tuple) -> list: nodes.append(attribute) for rel in self.node_relationships: if rel in relationships.keys(): - nodes.extend([node for node in relationships[rel] if node is not None]) + nodes.extend([node.strip() for node in relationships[rel]]) return nodes def gather_all_nodes_in_model(self, attr_rel_dict: dict) -> list: diff --git a/schematic/schemas/data_model_parser.py b/schematic/schemas/data_model_parser.py index a541eb3ed..da9498d44 100644 --- a/schematic/schemas/data_model_parser.py +++ b/schematic/schemas/data_model_parser.py @@ -243,7 +243,7 @@ def __init__( # Load relationships dictionary. self.rel_dict = self.dmr.define_data_model_relationships() - def parse_entry(self, rel_entry: any, id_jsonld_key: str, dn_label_dict:dict[str:str], model_jsonld:dict) -> Any: + def parse_entry(self, rel_entry: any, id_jsonld_key: str) -> Any: """Parse an input entry based on certain attributes Args: rel_entry: Given a single entry and relationship in a JSONLD data model, the recorded value @@ -256,7 +256,7 @@ def parse_entry(self, rel_entry: any, id_jsonld_key: str, dn_label_dict:dict[str parsed_rel_entry = rel_entry["@id"] # Parse list of dictionaries to make a list of entries with context stripped (will update this section when contexts added.) elif type(rel_entry) == list and type(rel_entry[0]) == dict: - parsed_rel_entry = self.convert_entry_to_dn_label([r[id_jsonld_key].split(":")[1] for r in rel_entry], model_jsonld) + parsed_rel_entry = [r[id_jsonld_key].split(":")[1] for r in rel_entry] # Strip context from string and convert true/false to bool elif type(rel_entry) == str: # Remove contexts and treat strings as appropriate. @@ -268,14 +268,29 @@ def parse_entry(self, rel_entry: any, id_jsonld_key: str, dn_label_dict:dict[str elif parsed_rel_entry.lower == "false": parsed_rel_entry = False else: - parsed_rel_entry=self.convert_entry_to_dn_label(rel_entry, model_jsonld) - + parsed_rel_entry = rel_entry # For anything else get that else: - parsed_rel_entry=self.convert_entry_to_dn_label(rel_entry, model_jsonld) - + parsed_rel_entry = rel_entry return parsed_rel_entry + ''' + def get_display_name_from_label(self, label, model_jsonld): + jsonld_keys_to_extract = ["label", "displayName"] + label_jsonld_key, dn_jsonld_key = [ + self.rel_dict[key]["jsonld_key"] for key in jsonld_keys_to_extract + ] + breakpoint() + for entry in model_jsonld: + # Get the attr key for the dictionary + if dn_jsonld_key in entry: + # The attr_key is the entry display name if one was recorded + attr_key = entry[dn_jsonld_key] + else: + # If not we wil use the get the label. + attr_key = entry[label_jsonld_key] + return attr_key + ''' def label_to_dn_dict(self, model_jsonld: list[dict]): """ Generate a dictionary of labels to display name, so can easily look up display names using the label. Args: @@ -302,6 +317,7 @@ def convert_entry_to_dn_label(self, parsed_rel_entry:Union[str,list], model_json """ # Get a dictionary of display_names mapped to labels dn_label_dict = self.label_to_dn_dict(model_jsonld=model_jsonld) + # Handle if using the display name as the label if type(parsed_rel_entry) == list: parsed_rel_entry = [dn_label_dict.get(entry) if dn_label_dict.get(entry) else entry for entry in parsed_rel_entry ] @@ -371,9 +387,11 @@ def gather_jsonld_attributes_relationships(self, model_jsonld: List[dict]) -> Di # If there is an entry parse it by type and add to the attr:relationships dictionary. if rel_entry: parsed_rel_entry = self.parse_entry( - rel_entry=rel_entry, id_jsonld_key=id_jsonld_key, dn_label_dict=dn_label_dict, model_jsonld=model_jsonld, + rel_entry=rel_entry, id_jsonld_key=id_jsonld_key ) rel_csv_header = self.rel_dict[rel_key]["csv_header"] + + #if rel_key == 'domainIncludes' or rel_key == 'subClassOf': if rel_key == 'domainIncludes': # In the JSONLD the domain includes field contains the ids of attributes that the current attribute is the property/parent of. # Because of this we need to handle these values differently. @@ -384,15 +402,16 @@ def gather_jsonld_attributes_relationships(self, model_jsonld: List[dict]) -> Di p_attr_key='' # Check if the parsed value is already a part of the attr_rel_dictionary for attr_dn, rels in attr_rel_dictionary.items(): - if parsed_val == attr_dn: + if parsed_val == rels["Relationships"].get('label'): p_attr_key = attr_dn attr_in_dict = True # If it is part of the dictionary update add current attribute as a property of the parsed value if attr_in_dict == True: + if not rel_csv_header in attr_rel_dictionary[p_attr_key]["Relationships"]: - attr_rel_dictionary[p_attr_key]["Relationships"].update({rel_csv_header:[entry[dn_jsonld_key]]}) + attr_rel_dictionary[p_attr_key]["Relationships"].update({rel_csv_header:[entry[label_jsonld_key]]}) else: - attr_rel_dictionary[p_attr_key]["Relationships"].update({rel_csv_header:[entry[dn_jsonld_key]]}) + attr_rel_dictionary[p_attr_key]["Relationships"][rel_csv_header].append(entry[label_jsonld_key]) # If the parsed_val is not already recorded in the dictionary, add it elif attr_in_dict == False: # Get the display name for the parsed value @@ -400,7 +419,6 @@ def gather_jsonld_attributes_relationships(self, model_jsonld: List[dict]) -> Di attr_rel_dictionary.update(attr_dict_template(p_attr_key)) attr_rel_dictionary[p_attr_key]["Relationships"].update({rel_csv_header:[entry[label_jsonld_key]]}) - else: attr_rel_dictionary[attr_key]["Relationships"].update( {rel_csv_header: parsed_rel_entry} @@ -415,7 +433,7 @@ def gather_jsonld_attributes_relationships(self, model_jsonld: List[dict]) -> Di # If there is an entry parset it by type and add to the attr:relationships dictionary. if rel_entry: parsed_rel_entry = self.parse_entry( - rel_entry=rel_entry, id_jsonld_key=id_jsonld_key, dn_label_dict=dn_label_dict, model_jsonld=model_jsonld, + rel_entry=rel_entry, id_jsonld_key=id_jsonld_key ) # Add relationships for each attribute and relationship to the dictionary attr_rel_dictionary[attr_key]["Relationships"].update( diff --git a/schematic/store/synapse.py b/schematic/store/synapse.py index c291b742e..bbc1bd295 100644 --- a/schematic/store/synapse.py +++ b/schematic/store/synapse.py @@ -170,9 +170,9 @@ class SynapseStorage(BaseStorage): def __init__( self, - token: Optional[str] = None, # optional parameter retrieved from browser cookie - access_token: Optional[str] = None, - project_scope: Optional[list] = None, + token: str = None, # optional parameter retrieved from browser cookie + access_token: str = None, + project_scope: List = None, ) -> None: """Initializes a SynapseStorage object. Args: @@ -309,7 +309,7 @@ def getPaginatedRestResults(self, currentUserId: str) -> Dict[str, str]: return all_results - def getStorageProjects(self, project_scope: List = None) -> list[tuple[str, str]]: + def getStorageProjects(self, project_scope: List = None) -> List[str]: """Gets all storage projects the current user has access to, within the scope of the 'storageFileview' attribute. Returns: @@ -357,7 +357,7 @@ def getStorageProjects(self, project_scope: List = None) -> list[tuple[str, str] return sorted_projects_list - def getStorageDatasetsInProject(self, projectId: str) -> list[tuple[str, str]]: + def getStorageDatasetsInProject(self, projectId: str) -> List[str]: """Gets all datasets in folder under a given storage project that the current user has access to. Args: @@ -707,9 +707,7 @@ def _get_file_entityIds(self, dataset_files: List, only_new_files: bool = False return files - def getProjectManifests( - self, projectId: str - ) -> list[tuple[tuple[str, str], tuple[str, str], tuple[str, str]]]: + def getProjectManifests(self, projectId: str) -> List[str]: """Gets all metadata manifest files across all datasets in a specified project. Returns: A list of datasets per project; metadata manifest Synapse ID for each dataset; and the corresponding schema component of the manifest @@ -1900,6 +1898,13 @@ def getDatasetAnnotations( def raise_final_error(retry_state): return retry_state.outcome.result() + @retry(stop = stop_after_attempt(5), + wait = wait_chain(*[wait_fixed(10) for i in range (2)] + + [wait_fixed(15) for i in range(2)] + + [wait_fixed(20)]), + retry=retry_if_exception_type(LookupError), + retry_error_callback = raise_final_error) + def checkIfinAssetView(self, syn_id) -> str: # get data in administrative fileview for this pipeline assetViewTable = self.getStorageFileviewTable() @@ -1909,12 +1914,6 @@ def checkIfinAssetView(self, syn_id) -> str: else: return False - @retry(stop = stop_after_attempt(5), - wait = wait_chain(*[wait_fixed(10) for i in range (2)] + - [wait_fixed(15) for i in range(2)] + - [wait_fixed(20)]), - retry=retry_if_exception_type(LookupError), - retry_error_callback = raise_final_error) def getDatasetProject(self, datasetId: str) -> str: """Get parent project for a given dataset ID. diff --git a/schematic/utils/validate_utils.py b/schematic/utils/validate_utils.py index 78c8277eb..3e694bce8 100644 --- a/schematic/utils/validate_utils.py +++ b/schematic/utils/validate_utils.py @@ -6,7 +6,6 @@ from schematic import LOADER from typing import List import numpy as np -from numbers import Number def validate_schema(schema): """Validate schema against schema.org standard""" @@ -76,22 +75,11 @@ def np_array_to_str_list(np_array): return np.char.mod('%d', np_array).tolist() def iterable_to_str_list(iterable): - """ - Parse an object into a list of strings - Accepts str, Number, and iterable inputs - """ + "Parse an iterable into a list of strings" + strlist = [] - # If object is a string, just return wrapped as a list - if isinstance(iterable, str): - return [iterable] - # If object is numberical, convert to string and wrap as a list - elif isinstance(iterable, Number): - return [str(iterable)] - # If the object is iterable and not a string, convert every element to string and wratp as a list - else: - strlist = [] - for element in iterable: - strlist.append(str(element)) + for element in iterable: + strlist.append(str(element)) return strlist \ No newline at end of file diff --git a/schematic/visualization/tangled_tree.py b/schematic/visualization/tangled_tree.py index 83635a39c..03bffd825 100644 --- a/schematic/visualization/tangled_tree.py +++ b/schematic/visualization/tangled_tree.py @@ -701,7 +701,7 @@ def get_node_layers_json(self, topological_gen, source_nodes, child_parents, par return layers_json - def save_outputs(self, save_file, layers_json, cn='', all_layers=None): + def save_outputs(self, save_file, layers_json, cn='', all_layers=[]): ''' Inputs: save_file (bool): Indicates whether to save a file locally or not.: @@ -715,8 +715,6 @@ def save_outputs(self, save_file, layers_json, cn='', all_layers=None): If save_file == False: Each string represents contains the layers for a single tangled tree. If save_file ==True: is an empty list. ''' - if all_layers is None: - all_layers = [] if save_file == True: if cn: output_file_name = f"{self.schema_abbr}_{self.figure_type}_{cn}_tangled_tree.json" diff --git a/schematic_api/api/routes.py b/schematic_api/api/routes.py index 736a0c2db..febdfe3f2 100644 --- a/schematic_api/api/routes.py +++ b/schematic_api/api/routes.py @@ -258,8 +258,6 @@ def get_manifest_route(schema_url: str, use_annotations: bool, dataset_ids=None, # call config_handler() config_handler(asset_view = asset_view) - temp_path = get_temp_model_path(schema_url=schema_url) - # Gather all data_types to make manifests for. all_args = connexion.request.args args_dict = dict(all_args.lists()) @@ -293,9 +291,86 @@ def get_manifest_route(schema_url: str, use_annotations: bool, dataset_ids=None, f"When submitting 'all manifests' as the data_type cannot also submit dataset_id. " f"Please check your submission and try again." ) - - all_results = ManifestGenerator.create_manifests(path_to_data_model=schema_url, output_format=output_format, data_types=data_type, title=title, access_token=access_token, dataset_ids=dataset_ids, strict=strict_validation, use_annotations=use_annotations) - + + data_model_parser = DataModelParser(path_to_data_model = schema_url) + + #Parse Model + parsed_data_model = data_model_parser.parse_model() + + # Instantiate DataModelGraph + data_model_grapher = DataModelGraph(parsed_data_model) + + # Generate graph + graph_data_model = data_model_grapher.generate_data_model_graph() + + def create_single_manifest(data_type, title, dataset_id=None, output_format=None, access_token=None, strict=strict_validation): + # create object of type ManifestGenerator + manifest_generator = ManifestGenerator( + path_to_json_ld=schema_url, + graph=graph_data_model, + title=title, + root=data_type, + use_annotations=use_annotations, + alphabetize_valid_values = 'ascending', + ) + + # if returning a dataframe + if output_format: + if "dataframe" in output_format: + output_format = "dataframe" + + result = manifest_generator.get_manifest( + dataset_id=dataset_id, sheet_url=True, output_format=output_format, access_token=access_token, strict=strict, + ) + + # return an excel file if output_format is set to "excel" + if output_format == "excel": + dir_name = os.path.dirname(result) + file_name = os.path.basename(result) + mimetype='application/vnd.openxmlformats-officedocument.spreadsheetml.sheet' + return send_from_directory(directory=dir_name, path=file_name, as_attachment=True, mimetype=mimetype, max_age=0) + + return result + + # Gather all returned result urls + all_results = [] + if data_type[0] == 'all manifests': + dmge = DataModelGraphExplorer(graph_data_model) + component_digraph = dmge.get_digraph_by_edge_type('requiresComponent') + components = component_digraph.nodes() + for component in components: + if title: + t = f'{title}.{component}.manifest' + else: + t = f'Example.{component}.manifest' + if output_format != "excel": + result = create_single_manifest(data_type=component, output_format=output_format, title=t, access_token=access_token) + all_results.append(result) + else: + app.logger.error('Currently we do not support returning multiple files as Excel format at once. Please choose a different output format. ') + else: + for i, dt in enumerate(data_type): + if not title: + t = f'Example.{dt}.manifest' + else: + if len(data_type) > 1: + t = f'{title}.{dt}.manifest' + else: + t = title + if dataset_ids: + # if a dataset_id is provided add this to the function call. + result = create_single_manifest(data_type=dt, dataset_id=dataset_ids[i], output_format=output_format, title=t, access_token=access_token) + else: + result = create_single_manifest(data_type=dt, output_format=output_format, title=t, access_token=access_token) + + # if output is pandas dataframe or google sheet url + if isinstance(result, str) or isinstance(result, pd.DataFrame): + all_results.append(result) + else: + if len(data_type) > 1: + app.logger.warning(f'Currently we do not support returning multiple files as Excel format at once. Only {t} would get returned. ') + return result + return all_results #####profile validate manifest route function diff --git a/tests/conftest.py b/tests/conftest.py index 55d100310..d3cc1b9e0 100644 --- a/tests/conftest.py +++ b/tests/conftest.py @@ -7,7 +7,6 @@ import pytest import pandas as pd from dotenv import load_dotenv, find_dotenv -from time import perf_counter from schematic.schemas.data_model_parser import DataModelParser from schematic.schemas.data_model_graph import DataModelGraph, DataModelGraphExplorer @@ -16,7 +15,6 @@ from schematic.configuration.configuration import CONFIG from schematic.utils.df_utils import load_df -from schematic.store.synapse import SynapseStorage load_dotenv() @@ -109,13 +107,3 @@ def helpers(): @pytest.fixture(scope="session") def config(): yield CONFIG - -@pytest.fixture(scope="session") -def synapse_store(request): - access_token = os.getenv("SYNAPSE_ACCESS_TOKEN") - if access_token: - synapse_store = SynapseStorage(access_token=access_token) - else: - synapse_store = SynapseStorage() - - yield synapse_store diff --git a/tests/data/example.model.jsonld b/tests/data/example.model.jsonld index a58d36323..f49346f0e 100644 --- a/tests/data/example.model.jsonld +++ b/tests/data/example.model.jsonld @@ -7,23 +7,6 @@ "xsd": "http://www.w3.org/2001/XMLSchema#" }, "@graph": [ - { - "@id": "bts:Component", - "@type": "rdfs:Class", - "rdfs:comment": "TBD", - "rdfs:label": "Component", - "rdfs:subClassOf": [ - { - "@id": "bts:Thing" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "Component", - "sms:required": "sms:true", - "sms:validationRules": [] - }, { "@id": "bts:Patient", "@type": "rdfs:Class", @@ -145,6 +128,23 @@ "sms:required": "sms:true", "sms:validationRules": [] }, + { + "@id": "bts:Component", + "@type": "rdfs:Class", + "rdfs:comment": "TBD", + "rdfs:label": "Component", + "rdfs:subClassOf": [ + { + "@id": "bts:Thing" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Component", + "sms:required": "sms:false", + "sms:validationRules": [] + }, { "@id": "bts:DataType", "@type": "rdfs:Class", diff --git a/tests/test_api.py b/tests/test_api.py index ccfb6ae7f..7eb768fe8 100644 --- a/tests/test_api.py +++ b/tests/test_api.py @@ -63,14 +63,12 @@ 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/mialy-defelice/data_models/main/example.model.jsonld" + data_model_jsonld ="https://raw.githubusercontent.com/Sage-Bionetworks/schematic/develop/tests/data/example.model.jsonld" yield data_model_jsonld @pytest.fixture(scope="class") def benchmark_data_model_jsonld(): - #benchmark_data_model_jsonld = "https://raw.githubusercontent.com/Sage-Bionetworks/schematic/develop/tests/data/example.single_rule.model.jsonld" - benchmark_data_model_jsonld = "https://raw.githubusercontent.com/mialy-defelice/data_models/main/example.single_rule.model.jsonld" + benchmark_data_model_jsonld = "https://raw.githubusercontent.com/Sage-Bionetworks/schematic/develop/tests/data/example.single_rule.model.jsonld" yield benchmark_data_model_jsonld def get_MockComponent_attribute(): @@ -78,8 +76,7 @@ def get_MockComponent_attribute(): Yield all of the mock conponent attributes one at a time TODO: pull in jsonld from fixture """ - #schema_url = "https://raw.githubusercontent.com/Sage-Bionetworks/schematic/develop/tests/data/example.single_rule.model.jsonld" - schema_url = "https://raw.githubusercontent.com/mialy-defelice/data_models/main/example.single_rule.model.jsonld" + schema_url = "https://raw.githubusercontent.com/Sage-Bionetworks/schematic/develop/tests/data/example.single_rule.model.jsonld" data_model_parser = DataModelParser(path_to_data_model = schema_url) #Parse Model parsed_data_model = data_model_parser.parse_model() @@ -562,7 +559,6 @@ def test_generate_manifest_file_based_annotations(self, client, use_annotations, # and also make sure that entityId column appears in the end assert google_sheet_df.columns.to_list()[-1] == "entityId" - assert sorted(google_sheet_df.columns.to_list()) == sorted(expected) # make sure Filename, entityId, and component get filled with correct value @@ -898,7 +894,6 @@ def test_visualize_attributes(self, client, data_model_jsonld): @pytest.mark.parametrize("figure_type", ["component", "dependency"]) def test_visualize_tangled_tree_layers(self, client, figure_type, data_model_jsonld): - # TODO: Determine a 2nd data model to use for this test, test both models sequentially, add checks for content of response params = { "schema_url": data_model_jsonld, "figure_type": figure_type diff --git a/tests/test_cli.py b/tests/test_cli.py index 5498a5900..f3cd19a59 100644 --- a/tests/test_cli.py +++ b/tests/test_cli.py @@ -64,7 +64,7 @@ def test_get_example_manifest_default(self, runner, helpers, config: Configurati config.load_config("config_example.yml") result = runner.invoke( - manifest, ["--config", config.config_path, "get", "--data_type", "Patient", "--path_to_data_model", data_model_jsonld] + manifest, ["--config", config.config_path, "get", "--data_type", "Patient", "--jsonld", data_model_jsonld] ) @@ -79,7 +79,7 @@ def test_get_example_manifest_csv(self, runner, helpers, config: Configuration, config.load_config("config_example.yml") result = runner.invoke( - manifest, ["--config", config.config_path, "get", "--data_type", "Patient", "--path_to_data_model", data_model_jsonld, "--output_csv", output_path] + manifest, ["--config", config.config_path, "get", "--data_type", "Patient", "--jsonld", data_model_jsonld, "--output_csv", output_path] ) assert result.exit_code == 0 self.assert_expected_file(result, output_path) @@ -91,7 +91,7 @@ def test_get_example_manifest_excel(self, runner, helpers, config: Configuration config.load_config("config_example.yml") result = runner.invoke( - manifest, ["--config", config.config_path, "get", "--data_type", "Patient", "--path_to_data_model", data_model_jsonld, "--output_xlsx", output_path] + manifest, ["--config", config.config_path, "get", "--data_type", "Patient", "--jsonld", data_model_jsonld, "--output_xlsx", output_path] ) assert result.exit_code == 0 diff --git a/tests/test_manifest.py b/tests/test_manifest.py index 417b86b47..07876b0fa 100644 --- a/tests/test_manifest.py +++ b/tests/test_manifest.py @@ -66,7 +66,7 @@ def manifest_generator(helpers, request): manifest_generator = ManifestGenerator( - path_to_data_model=path_to_data_model, + path_to_json_ld=path_to_data_model, graph=graph_data_model, root=data_type, use_annotations=use_annotations, @@ -121,7 +121,7 @@ def test_init(self, helpers): generator = ManifestGenerator( graph=graph_data_model, title="mock_title", - path_to_data_model=path_to_data_model, + path_to_json_ld=path_to_data_model, root = "Patient", ) @@ -147,7 +147,7 @@ def test_missing_root_error(self, helpers, data_type, exc, exc_message): # A LookupError should be raised and include message when the component cannot be found with pytest.raises(exc) as e: generator = ManifestGenerator( - path_to_data_model=helpers.get_data_path("example.model.jsonld"), + path_to_json_ld=helpers.get_data_path("example.model.jsonld"), graph=graph_data_model, root=data_type, use_annotations=False, @@ -173,7 +173,7 @@ def test_get_manifest_first_time(self, manifest): is_file_based = data_type in ["BulkRNA-seqAssay"] assert "Component" in output - assert is_file_based == ("entityId" in output) + assert is_file_based == ("eTag" in output) assert is_file_based == ("Filename" in output) assert (is_file_based and use_annotations) == ("confidence" in output) @@ -199,7 +199,7 @@ def test_get_manifest_first_time(self, manifest): assert output.shape[0] == 3 # Number of rows if use_annotations: assert output.shape[0] == 3 # Number of rows - assert "entityId" in output + assert "eTag" in output assert "confidence" in output assert output["Year of Birth"].tolist() == ["1980", "", ""] @@ -228,7 +228,7 @@ def test_get_manifest_excel(self, helpers, sheet_url, output_format, dataset_id) generator = ManifestGenerator( - path_to_data_model=path_to_data_model, + path_to_json_ld=path_to_data_model, graph=graph_data_model, root=data_type, use_annotations=False, @@ -280,7 +280,7 @@ def test_get_manifest_no_annos(self, helpers, dataset_id): # Instantiate object with use_annotations set to True generator = ManifestGenerator( - path_to_data_model=path_to_data_model, + path_to_json_ld=path_to_data_model, graph=graph_data_model, root=data_type, use_annotations=True, @@ -365,7 +365,7 @@ def test_add_root_to_component_without_additional_metadata(self, helpers, data_t graph_data_model = generate_graph_data_model(helpers, path_to_data_model=path_to_data_model) manifest_generator = ManifestGenerator( - path_to_data_model=path_to_data_model, + path_to_json_ld=path_to_data_model, graph=graph_data_model, root=data_type, ) @@ -385,7 +385,7 @@ def test_add_root_to_component_with_additional_metadata(self, helpers, additiona graph_data_model = generate_graph_data_model(helpers, path_to_data_model=path_to_data_model) manifest_generator = ManifestGenerator( - path_to_data_model=path_to_data_model, + path_to_json_ld=path_to_data_model, graph=graph_data_model, root="BulkRNA-seqAssay" ) @@ -437,7 +437,7 @@ def test_update_dataframe_with_existing_df(self, helpers, existing_manifest): # Instantiate the Manifest Generator. - generator = ManifestGenerator(path_to_data_model=path_to_data_model, + generator = ManifestGenerator(path_to_json_ld=path_to_data_model, graph=graph_data_model, root=data_type, use_annotations=False, diff --git a/tests/test_schemas.py b/tests/test_schemas.py index cccdb0208..7436712d1 100644 --- a/tests/test_schemas.py +++ b/tests/test_schemas.py @@ -543,7 +543,8 @@ def test_gather_nodes(self, helpers, data_model): # Make sure the nodes returned conform to expectations (values and order) ## The parsing records display names for relationships for CSV and labels for JSONLD, so the expectations are different between the two. - expected_nodes = [ + if DATA_MODEL_DICT[data_model] == "CSV": + expected_nodes = [ "Patient", "Patient ID", "Sex", @@ -552,6 +553,16 @@ def test_gather_nodes(self, helpers, data_model): "Component", "DataType", ] + elif DATA_MODEL_DICT[data_model] == "JSONLD": + expected_nodes = [ + "Patient", + "PatientID", + "Sex", + "YearofBirth", + "Diagnosis", + "Component", + "DataType", + ] assert nodes == expected_nodes diff --git a/tests/test_store.py b/tests/test_store.py index ed8990579..114ebcd43 100644 --- a/tests/test_store.py +++ b/tests/test_store.py @@ -10,22 +10,38 @@ import pytest from pandas.testing import assert_frame_equal from synapseclient import EntityViewSchema, Folder -from synapseclient.core.exceptions import SynapseHTTPError -from synapseclient.entity import File +from tenacity import (RetryError, Retrying, stop_after_attempt, + wait_random_exponential) +from schematic.models.metadata import MetadataModel +from schematic.store.base import BaseStorage +from schematic.store.synapse import SynapseStorage, DatasetFileView, ManifestDownload from schematic.schemas.data_model_parser import DataModelParser from schematic.schemas.data_model_graph import DataModelGraph, DataModelGraphExplorer from schematic.schemas.data_model_relationships import DataModelRelationships -from schematic.models.metadata import MetadataModel -from schematic.store.base import BaseStorage -from schematic.store.synapse import (DatasetFileView, - ManifestDownload,) + +from synapseclient.core.exceptions import SynapseHTTPError +from synapseclient.entity import File + + +from schematic.configuration.configuration import Configuration +from schematic.store.synapse import (DatasetFileView, ManifestDownload, + SynapseStorage) logging.basicConfig(level=logging.DEBUG) logger = logging.getLogger(__name__) +@pytest.fixture +def synapse_store(): + access_token = os.getenv("SYNAPSE_ACCESS_TOKEN") + if access_token: + synapse_store = SynapseStorage(access_token=access_token) + else: + synapse_store = SynapseStorage() + yield synapse_store + @pytest.fixture def test_download_manifest_id(): yield "syn51203973" @@ -112,8 +128,6 @@ def test_getFileAnnotations(self, synapse_store): @pytest.mark.parametrize('only_new_files',[True, False]) def test_get_file_entityIds(self, helpers, synapse_store, only_new_files): - #TODO: Automatically reset manifest at path specified below after each test - # so that subsequent runs do not affect each other manifest_path = "mock_manifests/test_BulkRNAseq.csv" dataset_files = synapse_store.getFilesInStorageDataset('syn39241199') @@ -121,8 +135,6 @@ def test_get_file_entityIds(self, helpers, synapse_store, only_new_files): # Prepare manifest is getting Ids for new files only manifest = helpers.get_data_frame(manifest_path) entityIds = pd.DataFrame({'entityId': ['syn39242580', 'syn51900502']}) - - # If this line errors out then the changes on the manifest file need to be discarded manifest = manifest.join(entityIds) # get entityIds for new files @@ -162,15 +174,24 @@ def test_annotation_submission(self, synapse_store, helpers, manifest_path, test # Instantiate DataModelGraphExplorer dmge = DataModelGraphExplorer(graph_data_model) - manifest_id = synapse_store.associateMetadataWithFiles( - dmge = dmge, - metadataManifestPath = helpers.get_data_path(manifest_path), - datasetId = datasetId, - manifest_record_type = manifest_record_type, - useSchemaLabel = True, - hideBlanks = True, - restrict_manifest = False, - ) + try: + for attempt in Retrying( + stop = stop_after_attempt(15), + wait = wait_random_exponential(multiplier=1,min=10,max=120), + retry_error_callback = raise_final_error + ): + with attempt: + manifest_id = synapse_store.associateMetadataWithFiles( + dmge = dmge, + metadataManifestPath = helpers.get_data_path(manifest_path), + datasetId = datasetId, + manifest_record_type = manifest_record_type, + useSchemaLabel = True, + hideBlanks = True, + restrict_manifest = False, + ) + except RetryError: + pass # Retrive annotations entity_id = helpers.get_data_frame(manifest_path)["entityId"][0] @@ -396,10 +417,10 @@ def test_createTable(self, helpers, synapse_store, config: Configuration, projec # associate metadata with files manifest_path = "mock_manifests/table_manifest.csv" inputModelLocaiton = helpers.get_data_path(os.path.basename(config.model_location)) + #sg = SchemaGenerator(inputModelLocaiton) # Instantiate DataModelParser data_model_parser = DataModelParser(path_to_data_model = inputModelLocaiton) - #Parse Model parsed_data_model = data_model_parser.parse_model() @@ -464,7 +485,7 @@ def test_replaceTable(self, helpers, synapse_store, config: Configuration, proje # Instantiate DataModelGraphExplorer dmge = DataModelGraphExplorer(graph_data_model) - # updating file view on synapse takes a long time + # updating file view on synapse takes a long time manifestId = synapse_store.associateMetadataWithFiles( dmge = dmge, metadataManifestPath = helpers.get_data_path(manifest_path), @@ -659,3 +680,8 @@ def test_entity_type_checking(self, synapse_store, entity_id, caplog): if entity_id == "syn27600053": for record in caplog.records: assert "You are using entity type: folder. Please provide a file ID" in record.message + + + + + diff --git a/tests/test_utils.py b/tests/test_utils.py index d9f06c845..cd5c27508 100644 --- a/tests/test_utils.py +++ b/tests/test_utils.py @@ -31,7 +31,7 @@ from schematic import LOADER from schematic.exceptions import (MissingConfigAndArgumentValueError, MissingConfigValueError) - +from schematic.store.synapse import SynapseStorage from schematic.utils import (cli_utils, df_utils, general, io_utils, validate_utils) from schematic.utils.general import (calculate_datetime, @@ -48,6 +48,15 @@ IN_GITHUB_ACTIONS = os.getenv("GITHUB_ACTIONS") +@pytest.fixture +def synapse_store(): + access_token = os.getenv("SYNAPSE_ACCESS_TOKEN") + if access_token: + synapse_store = SynapseStorage(access_token=access_token) + else: + synapse_store = SynapseStorage() + yield synapse_store + class TestGeneral: def test_clear_synapse_cache(self, tmp_path): # define location of mock synapse cache @@ -489,11 +498,11 @@ def test_csv_to_schemaorg(self, helpers, tmp_path): # saving updated schema.org schema actual_jsonld_path = tmp_path / "example.from_csv.model.jsonld" + #base_se.export_schema(actual_jsonld_path) export_schema(jsonld_data_model, actual_jsonld_path) # Compare both JSON-LD files expected_jsonld_path = helpers.get_data_path("example.model.jsonld") expected_jsonld = open(expected_jsonld_path).read() actual_jsonld = open(actual_jsonld_path).read() - assert expected_jsonld == actual_jsonld diff --git a/tests/test_validation.py b/tests/test_validation.py index df1211cfb..4e25c02c8 100644 --- a/tests/test_validation.py +++ b/tests/test_validation.py @@ -45,10 +45,6 @@ def get_rule_combinations(): continue class TestManifestValidation: - # check if suite has been created. If so, delete it - if os.path.exists("great_expectations/expectations/Manifest_test_suite.json"): - os.remove("great_expectations/expectations/Manifest_test_suite.json") - def test_valid_manifest(self,helpers,metadataModel): manifestPath = helpers.get_data_path("mock_manifests/Valid_Test_Manifest.csv") rootNode = 'MockComponent' @@ -383,7 +379,7 @@ def test_in_house_validation(self,helpers,dmge,metadataModel): invalid_entry = ['71738', '98085', '210065'], dmge = dmge, )[1] in warnings - + @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()) @@ -442,8 +438,7 @@ def test_rule_combinations(self, helpers, dmge, base_rule, second_rule, metadata dmge = dmge, jsonSchema = json_schema ) - - + #perform validation with no exceptions raised _, errors, warnings = validateManifest.validate_manifest_rules( manifest = manifest, @@ -451,3 +446,7 @@ def test_rule_combinations(self, helpers, dmge, base_rule, second_rule, metadata restrict_rules = False, project_scope = None, ) + + + + \ No newline at end of file