mustrd 0.2.0__py3-none-any.whl → 0.2.1__py3-none-any.whl

mustrd/mustrd.py

@@ -1,787 +1,787 @@
-"""
-MIT License
-
-Copyright (c) 2023 Semantic Partners Ltd
-
-Permission is hereby granted, free of charge, to any person obtaining a copy
-of this software and associated documentation files (the "Software"), to deal
-in the Software without restriction, including without limitation the rights
-to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
-copies of the Software, and to permit persons to whom the Software is
-furnished to do so, subject to the following conditions:
-
-The above copyright notice and this permission notice shall be included in all
-copies or substantial portions of the Software.
-
-THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
-IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
-FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
-AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
-LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
-OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
-SOFTWARE.
-"""
-
-import os
-from typing import Tuple, List
-
-import tomli
-from rdflib.plugins.parsers.notation3 import BadSyntax
-
-from . import logger_setup
-from dataclasses import dataclass
-
-from pyparsing import ParseException
-from pathlib import Path
-from requests import ConnectionError, ConnectTimeout, HTTPError, RequestException
-
-from rdflib import Graph, URIRef, RDF, XSD, SH, Literal
-
-from rdflib.compare import isomorphic, graph_diff
-import pandas
-
-from .namespace import MUST, TRIPLESTORE
-import requests
-import json
-from pandas import DataFrame
-
-from .spec_component import TableThenSpec, parse_spec_component, WhenSpec, ThenSpec
-from .utils import  is_json,get_mustrd_root
-from colorama import Fore, Style
-from tabulate import tabulate
-from collections import defaultdict
-from pyshacl import validate
-import logging 
-from http.client import HTTPConnection
-from .steprunner import upload_given, run_when
-
-log = logger_setup.setup_logger(__name__)
-
-requests.packages.urllib3.disable_warnings()
-requests.packages.urllib3.util.ssl_.DEFAULT_CIPHERS += ':HIGH:!DH:!aNULL'
-
-logging.basicConfig(format='%(asctime)s %(message)s', level=logging.INFO)
-
-
-def debug_requests_on():
-    '''Switches on logging of the requests module.'''
-    HTTPConnection.debuglevel = 1
-
-    logging.basicConfig()
-    logging.getLogger().setLevel(logging.DEBUG)
-    requests_log = logging.getLogger("requests.packages.urllib3")
-    requests_log.setLevel(logging.DEBUG)
-    requests_log.propagate = True
-
-def debug_requests_off():
-    '''Switches off logging of the requests module, might be some side-effects'''
-    HTTPConnection.debuglevel = 0
-
-    root_logger = logging.getLogger()
-    root_logger.setLevel(logging.WARNING)
-    root_logger.handlers = []
-    requests_log = logging.getLogger("requests.packages.urllib3")
-    requests_log.setLevel(logging.WARNING)
-    requests_log.propagate = False
-
-debug_requests_off()
-
-@dataclass
-class Specification:
-    spec_uri: URIRef
-    triple_store: dict
-    given: Graph
-    when: WhenSpec
-    then: ThenSpec
-    spec_file_name: str = "default.mustrd.ttl"
-
-
-@dataclass
-class GraphComparison:
-    in_expected_not_in_actual: Graph
-    in_actual_not_in_expected: Graph
-    in_both: Graph
-
-
-@dataclass
-class SpecResult:
-    spec_uri: URIRef
-    triple_store: URIRef
-
-
-@dataclass
-class SpecPassed(SpecResult):
-    pass
-
-
-@dataclass()
-class SpecPassedWithWarning(SpecResult):
-    warning: str
-
-
-@dataclass
-class SelectSpecFailure(SpecResult):
-    table_comparison: pandas.DataFrame
-    message: str
-
-
-@dataclass
-class ConstructSpecFailure(SpecResult):
-    graph_comparison: GraphComparison
-
-
-@dataclass
-class UpdateSpecFailure(SpecResult):
-    graph_comparison: GraphComparison
-
-
-@dataclass
-class SparqlParseFailure(SpecResult):
-    exception: ParseException
-
-
-@dataclass
-class SparqlExecutionError(SpecResult):
-    exception: Exception
-
-
-@dataclass
-class TripleStoreConnectionError(SpecResult):
-    exception: ConnectionError
-
-
-@dataclass
-class SpecSkipped(SpecResult):
-    message: str
-    spec_file_name: str = "default.mustrd.ttl"
-
-
-@dataclass
-class SparqlAction:
-    query: str
-
-
-@dataclass
-class SelectSparqlQuery(SparqlAction):
-    pass
-
-
-@dataclass
-class ConstructSparqlQuery(SparqlAction):
-    pass
-
-
-@dataclass
-class UpdateSparqlQuery(SparqlAction):
-    pass
-
-
-# https://github.com/Semantic-partners/mustrd/issues/19
-
-def validate_specs(run_config: dict, triple_stores: List, shacl_graph: Graph, ont_graph: Graph, file_name: str = "*")\
-        -> Tuple[List, Graph, List]:
-    spec_graph = Graph()
-    subject_uris = set()
-    focus_uris = set()
-    invalid_specs = []
-    ttl_files = list(run_config['spec_path'].glob(f'**/{file_name}.mustrd.ttl'))
-    ttl_files.sort()
-    log.info(f"Found {len(ttl_files)} {file_name}.mustrd.ttl files in {run_config['spec_path']}")
-
-    for file in ttl_files:
-        error_messages = []
-
-        log.info(f"Parse: {file}")
-        try:
-            file_graph = Graph().parse(file)
-        except BadSyntax as e:
-            template = "An exception of type {0} occurred when trying to parse a spec file. Arguments:\n{1!r}"
-            message = template.format(type(e).__name__, e.args)
-            log.error(message)
-            error_messages += [f"Could not extract spec from {file} due to exception of type "
-                               f"{type(e).__name__} when parsing file"]
-            continue
-        # run shacl validation
-        conforms, results_graph, results_text = validate(file_graph,
-                                                         shacl_graph=shacl_graph,
-                                                         ont_graph=ont_graph,
-                                                         inference='none',
-                                                         abort_on_first=False,
-                                                         allow_infos=False,
-                                                         allow_warnings=False,
-                                                         meta_shacl=False,
-                                                         advanced=True,
-                                                         js=False,
-                                                         debug=False)
-        if not conforms:
-            for msg in results_graph.objects(predicate=SH.resultMessage):
-                log.warning(f"{file_graph}")
-                log.warning(f"{msg} File: {file.name}")
-                error_messages += [f"{msg} File: {file.name}"]
-
-        # collect a list of uris of the tests in focus
-        for focus_uri in file_graph.subjects(predicate=MUST.focus, object=Literal("true", datatype=XSD.boolean)):
-            if focus_uri in focus_uris:
-                focus_uri = URIRef(str(focus_uri) + "_DUPLICATE")
-            focus_uris.add(focus_uri)
-
-        # make sure there are no duplicate test IRIs in the files
-        for subject_uri in file_graph.subjects(RDF.type, MUST.TestSpec):
-            if subject_uri in subject_uris:
-                log.warning(f"Duplicate subject URI found: {file.name} {subject_uri}. File will not be parsed.")
-                error_messages += [f"Duplicate subject URI found in {file.name}."]
-                subject_uri = URIRef(str(subject_uri) + "_DUPLICATE")
-            if len(error_messages) > 0:
-                error_messages.sort()
-                error_message = "\n".join(msg for msg in error_messages)
-                invalid_specs += [SpecSkipped(subject_uri, triple_store["type"], error_message, file.name) for triple_store in
-                                triple_stores]
-            else:
-                subject_uris.add(subject_uri)
-                this_spec_graph = Graph()
-                this_spec_graph.parse(file)
-                spec_uris_in_this_file = list(this_spec_graph.subjects(RDF.type, MUST.TestSpec))
-                for spec in spec_uris_in_this_file:
-                    # print(f"adding {tripleToAdd}")
-                    this_spec_graph.add([spec, MUST.specSourceFile, Literal(file)])
-                    this_spec_graph.add([spec, MUST.specFileName, Literal(file.name)])
-                # print(f"beforeadd: {spec_graph}" )
-                # print(f"beforeadd: {str(this_spec_graph.serialize())}" )
-                spec_graph += this_spec_graph
-
-
-    sourceFiles = list(spec_graph.subject_objects(MUST.specSourceFile))
-    # print(f"sourceFiles: {sourceFiles}")
-
-    valid_spec_uris = list(spec_graph.subjects(RDF.type, MUST.TestSpec))
-
-    if focus_uris:
-        invalid_focus_specs = []
-        for spec in invalid_specs:
-            if spec.spec_uri in focus_uris:
-                invalid_focus_specs += [spec]
-                focus_uris.remove(spec.spec_uri)
-        log.info(f"Collected {len(focus_uris)} focus test spec(s)")
-        return focus_uris, spec_graph, invalid_focus_specs
-    else:
-        log.info(f"Collected {len(valid_spec_uris)} valid test spec(s)")   
-        return valid_spec_uris, spec_graph, invalid_specs
-
-
-def get_specs(spec_uris: List[URIRef], spec_graph: Graph, triple_stores: List[dict],
-              run_config: dict):
-    specs = []
-    skipped_results = []
-    try:
-        for triple_store in triple_stores:
-            if "error" in triple_store:
-                log.error(f"{triple_store['error']}. No specs run for this triple store.")
-                skipped_results += [SpecSkipped(spec_uri, triple_store['type'], triple_store['error'], get_spec_file(spec_uri, spec_graph)) for spec_uri in
-                                    spec_uris]
-            else:
-                for spec_uri in spec_uris:
-                    try:
-                        specs += [get_spec(spec_uri, spec_graph, run_config, triple_store)]
-                    except (ValueError, FileNotFoundError, ConnectionError) as e:
-                        skipped_results += [SpecSkipped(spec_uri, triple_store['type'], e, get_spec_file(spec_uri, spec_graph))]
-
-    except (BadSyntax, FileNotFoundError) as e:
-        template = "An exception of type {0} occurred when trying to parse the triple store configuration file. " \
-                   "Arguments:\n{1!r}"
-        message = template.format(type(e).__name__, e.args)
-        log.error(message)
-        log.error("No specifications will be run.")
-
-    log.info(f"Extracted {len(specs)} specifications that will be run")
-    return specs, skipped_results
-
-
-def run_specs(specs) -> List[SpecResult]:
-    results = []
-    # https://github.com/Semantic-partners/mustrd/issues/115
-    for specification in specs:
-        results.append(run_spec(specification))
-    return results
-
-def get_spec_file(spec_uri: URIRef, spec_graph: Graph):
-    return str(spec_graph.value(subject = spec_uri, predicate = MUST.specFileName, default = "default.mustrd.ttl"))
-
-def get_spec(spec_uri: URIRef, spec_graph: Graph, run_config: dict, mustrd_triple_store: dict = None) -> Specification:
-    try:
-        if mustrd_triple_store is None:
-            mustrd_triple_store = {"type": TRIPLESTORE.RdfLib}
-        components = []
-        for predicate in MUST.given, MUST.when, MUST.then:
-            components.append(parse_spec_component(subject=spec_uri,
-                                                predicate=predicate,
-                                                spec_graph=spec_graph,
-                                                run_config=run_config,
-                                                mustrd_triple_store=mustrd_triple_store))
-
-        spec_file_name = get_spec_file(spec_uri, spec_graph)
-        # https://github.com/Semantic-partners/mustrd/issues/92
-        return Specification(spec_uri, mustrd_triple_store, components[0].value, components[1], components[2], spec_file_name)
-    
-    except (ValueError, FileNotFoundError) as e:
-        template = "An exception of type {0} occurred. Arguments:\n{1!r}"
-        message = template.format(type(e).__name__, e.args)
-        log.exception(message)
-        raise
-    except ConnectionError as e:
-        log.error(e)
-        raise
-
-
-def check_result(spec, result):
-    if type(spec.then) == TableThenSpec:
-        return table_comparison(result, spec)
-    else:
-        graph_compare = graph_comparison(spec.then.value, result)
-        if isomorphic(result, spec.then.value):
-            return SpecPassed(spec.spec_uri, spec.triple_store["type"])
-        else:
-            if spec.when[0].queryType == MUST.ConstructSparql:
-                return ConstructSpecFailure(spec.spec_uri, spec.triple_store["type"], graph_compare)
-            else:
-                return UpdateSpecFailure(spec.spec_uri, spec.triple_store["type"], graph_compare)
-
-
-def run_spec(spec: Specification) -> SpecResult:
-    spec_uri = spec.spec_uri
-    triple_store = spec.triple_store
-    # close_connection = True
-    log.debug(f"run_when {spec_uri=}, {triple_store=}, {spec.given=}, {spec.when=}, {spec.then=}")
-    if spec.given:
-        given_as_turtle = spec.given.serialize(format="turtle")
-        log.debug(f"{given_as_turtle}")
-        upload_given(triple_store, spec.given)
-    else:
-        if triple_store['type'] == TRIPLESTORE.RdfLib:
-            return SpecSkipped(spec_uri, triple_store['type'], "Unable to run Inherited State tests on Rdflib")
-    try:
-        for when in spec.when:
-            log.info(f"Running {when.queryType} spec {spec_uri} on {triple_store['type']}")
-            try:
-                result = run_when(spec_uri, triple_store, when)
-            except ParseException as e:
-                return SparqlParseFailure(spec_uri, triple_store["type"], e)
-            except NotImplementedError as ex:
-                return SpecSkipped(spec_uri, triple_store["type"], ex.args[0])
-        return check_result(spec, result)
-    except (ConnectionError, TimeoutError, HTTPError, ConnectTimeout, OSError) as e:
-        # close_connection = False
-        template = "An exception of type {0} occurred. Arguments:\n{1!r}"
-        message = template.format(type(e).__name__, e.args)
-        log.error(message)
-        return TripleStoreConnectionError(spec_uri, triple_store["type"], message)
-    except (TypeError, RequestException) as e:
-        log.error(f"{type(e)} {e}")
-        return SparqlExecutionError(spec_uri, triple_store["type"], e)
-
-    # https://github.com/Semantic-partners/mustrd/issues/78
-    # finally:
-    #     if type(mustrd_triple_store) == MustrdAnzo and close_connection:
-    #         mustrd_triple_store.clear_graph()
-
-def get_triple_store_graph(triple_store_graph_path: Path, secrets: str):
-    if secrets:
-        return Graph().parse(triple_store_graph_path).parse(data = secrets)
-    else:
-        secret_path = triple_store_graph_path.parent / Path(triple_store_graph_path.stem + "_secrets" + triple_store_graph_path.suffix)
-        return Graph().parse(triple_store_graph_path).parse(secret_path)
-    
-
-def get_triple_stores(triple_store_graph: Graph) -> list[dict]:
-    triple_stores = []
-    shacl_graph = Graph().parse(Path(os.path.join(get_mustrd_root(), "model/triplestoreshapes.ttl")))
-    ont_graph = Graph().parse(Path(os.path.join(get_mustrd_root(), "model/triplestoreOntology.ttl")))
-    conforms, results_graph, results_text = validate(
-            data_graph= triple_store_graph,
-            shacl_graph = shacl_graph,
-            ont_graph  = ont_graph,
-            advanced= True,
-            inference= 'none'
-        )
-    if not conforms:
-        raise ValueError(f"Triple store configuration not conform to the shapes. SHACL report: {results_text}", results_graph)
-    for triple_store_config, rdf_type, triple_store_type in triple_store_graph.triples((None, RDF.type, None)):
-        triple_store = {}
-        triple_store["type"] = triple_store_type
-        triple_store["uri"] = triple_store_config
-        # Anzo graph via anzo
-        if triple_store_type == TRIPLESTORE.Anzo:
-            triple_store["url"] = triple_store_graph.value(subject=triple_store_config, predicate=TRIPLESTORE.url)
-            triple_store["port"] = triple_store_graph.value(subject=triple_store_config, predicate=TRIPLESTORE.port)
-            try:
-                triple_store["username"] = str(triple_store_graph.value(subject=triple_store_config, predicate=TRIPLESTORE.username))
-                triple_store["password"] = str(triple_store_graph.value(subject=triple_store_config, predicate=TRIPLESTORE.password))
-            except (FileNotFoundError, ValueError) as e:
-                triple_store["error"] = e
-            triple_store["gqe_uri"] = triple_store_graph.value(subject=triple_store_config, predicate=TRIPLESTORE.gqeURI)
-            triple_store["input_graph"] = triple_store_graph.value(subject=triple_store_config,
-                                                                   predicate=TRIPLESTORE.inputGraph)
-            triple_store["output_graph"] = triple_store_graph.value(subject=triple_store_config,
-                                                                   predicate=TRIPLESTORE.outputGraph)
-            try:
-                check_triple_store_params(triple_store, ["url", "port", "username", "password", "input_graph"])
-            except ValueError as e:
-                triple_store["error"] = e
-        # GraphDB
-        elif triple_store_type == TRIPLESTORE.GraphDb:
-            triple_store["url"] = triple_store_graph.value(subject=triple_store_config, predicate=TRIPLESTORE.url)
-            triple_store["port"] = triple_store_graph.value(subject=triple_store_config, predicate=TRIPLESTORE.port)
-            try:
-                triple_store["username"] = str(triple_store_graph.value(subject=triple_store_config, predicate=TRIPLESTORE.username))
-                triple_store["password"] = str(triple_store_graph.value(subject=triple_store_config, predicate=TRIPLESTORE.password))
-            except (FileNotFoundError, ValueError) as e:
-                log.error(f"Credential retrieval failed {e}")
-                triple_store["error"] = e
-            triple_store["repository"] = triple_store_graph.value(subject=triple_store_config,
-                                                                  predicate=TRIPLESTORE.repository)
-            triple_store["input_graph"] = triple_store_graph.value(subject=triple_store_config,
-                                                                   predicate=TRIPLESTORE.inputGraph)
-
-            try:
-                check_triple_store_params(triple_store, ["url", "port", "repository"])
-            except ValueError as e:
-                triple_store["error"] = e
-        elif triple_store_type != TRIPLESTORE.RdfLib:
-            triple_store["error"] = f"Triple store not implemented: {triple_store_type}"
-
-        triple_stores.append(triple_store)
-    return triple_stores
-
-
-def check_triple_store_params(triple_store: dict, required_params: List[str]):
-    missing_params = [param for param in required_params if triple_store.get(param) is None]
-    if missing_params:
-        raise ValueError(f"Cannot establish connection to {triple_store['type']}. "
-                         f"Missing required parameter(s): {', '.join(missing_params)}.")
-
-
-def get_credential_from_file(triple_store_name: URIRef, credential: str, config_path: Literal) -> str:
-    log.info(f"get_credential_from_file {triple_store_name}, {credential}, {config_path}")
-    if config_path is None:
-        raise ValueError(f"Cannot establish connection defined in {triple_store_name}. "
-                         f"Missing required parameter: {credential}.")
-    # if os.path.isrelative(config_path)
-    # project_root = get_project_root()
-    path = Path(config_path)
-    log.info(f"get_credential_from_file {path}")
-
-    if not os.path.isfile(path):
-        log.error(f"couldn't find {path}")
-        raise FileNotFoundError(f"Credentials config file not found: {path}")
-    try:
-        with open(path, "rb") as f:
-            config = tomli.load(f)
-    except tomli.TOMLDecodeError as e:
-        log.error(f"config error {path} {e}")
-        raise ValueError(f"Error reading credentials config file: {e}")
-    return config[str(triple_store_name)][credential]
-
-# Convert sparql json query results as defined in https://www.w3.org/TR/rdf-sparql-json-res/
-def json_results_to_panda_dataframe(result: str) -> pandas.DataFrame:
-    json_result = json.loads(result)
-    frames = DataFrame()
-    for binding in json_result["results"]["bindings"]:
-        columns = []
-        values = []
-        for key in binding:
-            value_object = binding[key]
-            columns.append(key)
-            values.append(str(value_object["value"]))
-            columns.append(key + "_datatype")
-            if "type" in value_object and value_object["type"] == "literal":
-                literal_type = str(XSD.string)
-                if "datatype" in value_object:
-                    literal_type = value_object["datatype"]
-                values.append(literal_type)
-            else:
-                values.append(str(XSD.anyURI))
-
-        frames = pandas.concat(objs=[frames, pandas.DataFrame([values], columns=columns)], ignore_index=True)
-        frames.fillna('', inplace=True)
-
-        if frames.size == 0:
-            frames = pandas.DataFrame()
-    return frames
-
-
-# https://github.com/Semantic-partners/mustrd/issues/110
-# https://github.com/Semantic-partners/mustrd/issues/52
-def table_comparison(result: str, spec: Specification) -> SpecResult:
-    warning = None
-    order_list = ["order by ?", "order by desc", "order by asc"]
-    ordered_result = any(pattern in spec.when[0].value.lower() for pattern in order_list)
-    then = spec.then.value
-    try:
-        if is_json(result):
-            df = json_results_to_panda_dataframe(result)
-            columns = list(df.columns)
-        else:
-            raise ParseException
-        sorted_columns = sorted(columns)
-        sorted_then_cols = sorted(list(then))
-        if not df.empty:
-
-            if not ordered_result:
-                df.sort_values(by=columns[::2], inplace=True)
-                df.reset_index(inplace=True, drop=True)
-                if spec.then.ordered:
-                    warning = f"sh:order in {spec.spec_uri} is ignored, no ORDER BY in query"
-                    log.warning(warning)
-
-            # Scenario 1: expected no result but got a result
-            if then.empty:
-                message = f"Expected 0 row(s) and 0 column(s), got {df.shape[0]} row(s) and {round(df.shape[1] / 2)} column(s)"
-                empty_then = create_empty_dataframe_with_columns(df)
-                df_diff = empty_then.compare(df, result_names=("expected", "actual"))
-
-            else:
-                # Scenario 2: expected a result and got a result
-                # pandas.set_option('display.max_columns', None)
-                message = f"Expected {then.shape[0]} row(s) and {round(then.shape[1] / 2)} column(s), " \
-                          f"got {df.shape[0]} row(s) and {round(df.shape[1] / 2)} column(s)"
-                if ordered_result is True and not spec.then.ordered:
-                    message += ". Actual result is ordered, must:then must contain sh:order on every row."
-                    return SelectSpecFailure(spec.spec_uri, spec.triple_store["type"], None, message)
-                    # if df.shape == then.shape and (df.columns == then.columns).all():
-                    #     df_diff = then.compare(df, result_names=("expected", "actual"))
-                    #     if df_diff.empty:
-                    #         df_diff = df
-                    #         print(df_diff.to_markdown())
-                    # else:
-                    #     df_diff = construct_df_diff(df, then)
-                    #     print(df_diff.to_markdown())
-                else:
-                    if len(columns) == len(then.columns):
-                        if sorted_columns == sorted_then_cols:
-                            then = then[columns]
-                            if not ordered_result:
-                                then.sort_values(by=columns[::2], inplace=True)
-                                then.reset_index(drop=True, inplace=True)
-                            if df.shape == then.shape and (df.columns == then.columns).all():
-                                df_diff = then.compare(df, result_names=("expected", "actual"))
-                            else:
-                                df_diff = construct_df_diff(df, then)
-
-                        else:
-                            then = then[sorted_then_cols]
-                            df = df[sorted_columns]
-                            df_diff = construct_df_diff(df, then)
-                    else:
-
-                        then = then[sorted_then_cols]
-                        df = df[sorted_columns]
-                        df_diff = construct_df_diff(df, then)
-        else:
-
-            if then.empty:
-                # Scenario 3: expected no result, got no result
-                message = f"Expected 0 row(s) and 0 column(s), got 0 row(s) and 0 column(s)"
-                df = pandas.DataFrame()
-            else:
-                # Scenario 4: expected a result, but got an empty result
-                message = f"Expected {then.shape[0]} row(s) and {round(then.shape[1] / 2)} column(s), got 0 row(s) and 0 column(s)"
-                then = then[sorted_then_cols]
-                df = create_empty_dataframe_with_columns(then)
-            df_diff = then.compare(df, result_names=("expected", "actual"))
-            print(df_diff.to_markdown())
-
-        if df_diff.empty:
-            if warning:
-                return SpecPassedWithWarning(spec.spec_uri, spec.triple_store["type"], warning)
-            else:
-                return SpecPassed(spec.spec_uri, spec.triple_store["type"])
-        else:
-            # message += f"\nexpected:\n{then}\nactual:{df}"
-            log.error(message)
-            # print(spec.spec_uri)
-            # print("actual:")
-            # print(then)
-            # print("expected:")
-            # print(df)
-            return SelectSpecFailure(spec.spec_uri, spec.triple_store["type"], df_diff, message)
-
-    except ParseException as e:
-        return SparqlParseFailure(spec.spec_uri, spec.triple_store["type"], e)
-    except NotImplementedError as ex:
-        return SpecSkipped(spec.spec_uri, spec.triple_store["type"], ex)
-
-
-def graph_comparison(expected_graph: Graph, actual_graph: Graph) -> GraphComparison:
-    diff = graph_diff(expected_graph, actual_graph)
-    in_both = diff[0]
-    in_expected = diff[1]
-    in_actual = diff[2]
-    in_expected_not_in_actual = (in_expected - in_actual)
-    in_actual_not_in_expected = (in_actual - in_expected)
-    return GraphComparison(in_expected_not_in_actual, in_actual_not_in_expected, in_both)
-
-
-def get_then_update(spec_uri: URIRef, spec_graph: Graph) -> Graph:
-    then_query = f"""
-    prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> 
-
-    CONSTRUCT {{ ?s ?p ?o }}
-    {{
-        <{spec_uri}> <{MUST.then}> 
-            a <{MUST.StatementsDataset}> ;
-            <{MUST.hasStatement}> [
-                a rdf:Statement ;
-                rdf:subject ?s ;
-                rdf:predicate ?p ;
-                rdf:object ?o ;
-            ] ; ] 
-    }}
-    """
-    expected_results = spec_graph.query(then_query).graph
-
-    return expected_results
-
-
-def calculate_row_difference(df1: pandas.DataFrame,
-                             df2: pandas.DataFrame) -> pandas.DataFrame:
-    df_all = df1.merge(df2.drop_duplicates(), how='left', indicator=True)
-    actual_rows = df_all[df_all['_merge'] == 'left_only']
-    actual_rows = actual_rows.drop('_merge', axis=1)
-    return actual_rows
-
-
-def construct_df_diff(df: pandas.DataFrame,
-                      then: pandas.DataFrame) -> pandas.DataFrame:
-    actual_rows = calculate_row_difference(df, then)
-    expected_rows = calculate_row_difference(then, df)
-    actual_columns = df.columns.difference(then.columns)
-    expected_columns = then.columns.difference(df.columns)
-
-    df_diff = pandas.DataFrame()
-    modified_df = df
-    modified_then = then
-
-    if actual_columns.size > 0:
-        modified_then = modified_then.reindex(modified_then.columns.to_list() + actual_columns.to_list(), axis=1)
-        modified_then[actual_columns.to_list()] = modified_then[actual_columns.to_list()].fillna('')
-
-    if expected_columns.size > 0:
-        modified_df = modified_df.reindex(modified_df.columns.to_list() + expected_columns.to_list(), axis=1)
-        modified_df[expected_columns.to_list()] = modified_df[expected_columns.to_list()].fillna('')
-
-    modified_df = modified_df.reindex(modified_then.columns, axis=1)
-
-    if df.shape[0] != then.shape[0] and df.shape[1] != then.shape[1]:
-        # take modified columns and add rows
-        actual_rows = calculate_row_difference(modified_df, modified_then)
-        expected_rows = calculate_row_difference(modified_then, modified_df)
-        df_diff = generate_row_diff(actual_rows, expected_rows)
-    elif actual_rows.shape[0] > 0 or expected_rows.shape[0] > 0:
-        df_diff = generate_row_diff(actual_rows, expected_rows)
-    elif actual_columns.size > 0 or expected_columns.size > 0:
-        df_diff = modified_then.compare(modified_df, result_names=("expected", "actual"), keep_shape=True,
-                                        keep_equal=True)
-    df_diff.fillna("", inplace=True)
-    return df_diff
-
-
-def generate_row_diff(actual_rows: pandas.DataFrame, expected_rows: pandas.DataFrame) -> pandas.DataFrame:
-    df_diff_actual_rows = pandas.DataFrame()
-    df_diff_expected_rows = pandas.DataFrame()
-
-    if actual_rows.shape[0] > 0:
-        empty_actual_copy = create_empty_dataframe_with_columns(actual_rows)
-        df_diff_actual_rows = empty_actual_copy.compare(actual_rows, result_names=("expected", "actual"))
-
-    if expected_rows.shape[0] > 0:
-        empty_expected_copy = create_empty_dataframe_with_columns(expected_rows)
-        df_diff_expected_rows = expected_rows.compare(empty_expected_copy, result_names=("expected", "actual"))
-
-    df_diff_rows = pandas.concat([df_diff_actual_rows, df_diff_expected_rows], ignore_index=True)
-    return df_diff_rows
-
-
-def create_empty_dataframe_with_columns(df: pandas.DataFrame) -> pandas.DataFrame:
-    empty_copy = pandas.DataFrame().reindex_like(df)
-    empty_copy.fillna("", inplace=True)
-    return empty_copy
-
-
-def review_results(results: List[SpecResult], verbose: bool) -> None:
-    print("===== Result Overview =====")
-    # Init dictionaries
-    status_dict = defaultdict(lambda: defaultdict(int))
-    status_counts = defaultdict(lambda: defaultdict(int))
-    colours = {SpecPassed: Fore.GREEN, SpecPassedWithWarning: Fore.YELLOW, SpecSkipped: Fore.YELLOW}
-    # Populate dictionaries from results
-    for result in results:
-        status_counts[result.triple_store][type(result)] += 1
-        status_dict[result.spec_uri][result.triple_store] = type(result)
-
-    # Get the list of statuses and list of unique triple stores
-    statuses = list(status for inner_dict in status_dict.values() for status in inner_dict.values())
-    triple_stores = list(set(status for inner_dict in status_dict.values() for status in inner_dict.keys()))
-
-    # Convert dictionaries to list for tabulate
-    table_rows = [[spec_uri] + [
-        f"{colours.get(status_dict[spec_uri][triple_store], Fore.RED)}{status_dict[spec_uri][triple_store].__name__}{Style.RESET_ALL}"
-        for triple_store in triple_stores] for spec_uri in set(status_dict.keys())]
-
-    status_rows = [[f"{colours.get(status, Fore.RED)}{status.__name__}{Style.RESET_ALL}"] +
-                   [f"{colours.get(status, Fore.RED)}{status_counts[triple_store][status]}{Style.RESET_ALL}"
-                    for triple_store in triple_stores] for status in set(statuses)]
-
-    # Display tables with tabulate
-    print(tabulate(table_rows, headers=['Spec Uris / triple stores'] + triple_stores, tablefmt="pretty"))
-    print(tabulate(status_rows, headers=['Status / triple stores'] + triple_stores, tablefmt="pretty"))
-
-    pass_count = statuses.count(SpecPassed)
-    warning_count = statuses.count(SpecPassedWithWarning)
-    skipped_count = statuses.count(SpecSkipped)
-    fail_count = len(
-        list(filter(lambda status: status not in [SpecPassed, SpecPassedWithWarning, SpecSkipped], statuses)))
-
-    if fail_count:
-        overview_colour = Fore.RED
-    elif warning_count or skipped_count:
-        overview_colour = Fore.YELLOW
-    else:
-        overview_colour = Fore.GREEN
-
-    logger_setup.flush()
-    print(f"{overview_colour}===== {fail_count} failures, {skipped_count} skipped, {Fore.GREEN}{pass_count} passed, "
-          f"{overview_colour}{warning_count} passed with warnings =====")
-
-    if verbose and (fail_count or warning_count or skipped_count):
-        for res in results:
-            if type(res) == UpdateSpecFailure:
-                print(f"{Fore.RED}Failed {res.spec_uri} {res.triple_store}")
-                print(f"{Fore.BLUE} In Expected Not In Actual:")
-                print(res.graph_comparison.in_expected_not_in_actual.serialize(format="ttl"))
-                print()
-                print(f"{Fore.RED} in_actual_not_in_expected")
-                print(res.graph_comparison.in_actual_not_in_expected.serialize(format="ttl"))
-                print(f"{Fore.GREEN} in_both")
-                print(res.graph_comparison.in_both.serialize(format="ttl"))
-
-            if type(res) == SelectSpecFailure:
-                print(f"{Fore.RED}Failed {res.spec_uri} {res.triple_store}")
-                print(res.message)
-                print(res.table_comparison.to_markdown())
-            if type(res) == ConstructSpecFailure or type(res) == UpdateSpecFailure:
-                print(f"{Fore.RED}Failed {res.spec_uri} {res.triple_store}")
-            if type(res) == SpecPassedWithWarning:
-                print(f"{Fore.YELLOW}Passed with warning {res.spec_uri} {res.triple_store}")
-                print(res.warning)
-            if type(res) == TripleStoreConnectionError or type(res) == SparqlExecutionError or \
-                    type(res) == SparqlParseFailure:
-                print(f"{Fore.RED}Failed {res.spec_uri} {res.triple_store}")
-                print(res.exception)
-            if type(res) == SpecSkipped:
-                print(f"{Fore.YELLOW}Skipped {res.spec_uri} {res.triple_store}")
-                print(res.message)
-
-
-
-    
-
-
+"""
+MIT License
+
+Copyright (c) 2023 Semantic Partners Ltd
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.
+"""
+
+import os
+from typing import Tuple, List
+
+import tomli
+from rdflib.plugins.parsers.notation3 import BadSyntax
+
+from . import logger_setup
+from dataclasses import dataclass
+
+from pyparsing import ParseException
+from pathlib import Path
+from requests import ConnectionError, ConnectTimeout, HTTPError, RequestException
+
+from rdflib import Graph, URIRef, RDF, XSD, SH, Literal
+
+from rdflib.compare import isomorphic, graph_diff
+import pandas
+
+from .namespace import MUST, TRIPLESTORE
+import requests
+import json
+from pandas import DataFrame
+
+from .spec_component import TableThenSpec, parse_spec_component, WhenSpec, ThenSpec
+from .utils import  is_json,get_mustrd_root
+from colorama import Fore, Style
+from tabulate import tabulate
+from collections import defaultdict
+from pyshacl import validate
+import logging 
+from http.client import HTTPConnection
+from .steprunner import upload_given, run_when
+
+log = logger_setup.setup_logger(__name__)
+
+requests.packages.urllib3.disable_warnings()
+requests.packages.urllib3.util.ssl_.DEFAULT_CIPHERS += ':HIGH:!DH:!aNULL'
+
+logging.basicConfig(format='%(asctime)s %(message)s', level=logging.INFO)
+
+
+def debug_requests_on():
+    '''Switches on logging of the requests module.'''
+    HTTPConnection.debuglevel = 1
+
+    logging.basicConfig()
+    logging.getLogger().setLevel(logging.DEBUG)
+    requests_log = logging.getLogger("requests.packages.urllib3")
+    requests_log.setLevel(logging.DEBUG)
+    requests_log.propagate = True
+
+def debug_requests_off():
+    '''Switches off logging of the requests module, might be some side-effects'''
+    HTTPConnection.debuglevel = 0
+
+    root_logger = logging.getLogger()
+    root_logger.setLevel(logging.WARNING)
+    root_logger.handlers = []
+    requests_log = logging.getLogger("requests.packages.urllib3")
+    requests_log.setLevel(logging.WARNING)
+    requests_log.propagate = False
+
+debug_requests_off()
+
+@dataclass
+class Specification:
+    spec_uri: URIRef
+    triple_store: dict
+    given: Graph
+    when: WhenSpec
+    then: ThenSpec
+    spec_file_name: str = "default.mustrd.ttl"
+
+
+@dataclass
+class GraphComparison:
+    in_expected_not_in_actual: Graph
+    in_actual_not_in_expected: Graph
+    in_both: Graph
+
+
+@dataclass
+class SpecResult:
+    spec_uri: URIRef
+    triple_store: URIRef
+
+
+@dataclass
+class SpecPassed(SpecResult):
+    pass
+
+
+@dataclass()
+class SpecPassedWithWarning(SpecResult):
+    warning: str
+
+
+@dataclass
+class SelectSpecFailure(SpecResult):
+    table_comparison: pandas.DataFrame
+    message: str
+
+
+@dataclass
+class ConstructSpecFailure(SpecResult):
+    graph_comparison: GraphComparison
+
+
+@dataclass
+class UpdateSpecFailure(SpecResult):
+    graph_comparison: GraphComparison
+
+
+@dataclass
+class SparqlParseFailure(SpecResult):
+    exception: ParseException
+
+
+@dataclass
+class SparqlExecutionError(SpecResult):
+    exception: Exception
+
+
+@dataclass
+class TripleStoreConnectionError(SpecResult):
+    exception: ConnectionError
+
+
+@dataclass
+class SpecSkipped(SpecResult):
+    message: str
+    spec_file_name: str = "default.mustrd.ttl"
+
+
+@dataclass
+class SparqlAction:
+    query: str
+
+
+@dataclass
+class SelectSparqlQuery(SparqlAction):
+    pass
+
+
+@dataclass
+class ConstructSparqlQuery(SparqlAction):
+    pass
+
+
+@dataclass
+class UpdateSparqlQuery(SparqlAction):
+    pass
+
+
+# https://github.com/Semantic-partners/mustrd/issues/19
+
+def validate_specs(run_config: dict, triple_stores: List, shacl_graph: Graph, ont_graph: Graph, file_name: str = "*")\
+        -> Tuple[List, Graph, List]:
+    spec_graph = Graph()
+    subject_uris = set()
+    focus_uris = set()
+    invalid_specs = []
+    ttl_files = list(run_config['spec_path'].glob(f'**/{file_name}.mustrd.ttl'))
+    ttl_files.sort()
+    log.info(f"Found {len(ttl_files)} {file_name}.mustrd.ttl files in {run_config['spec_path']}")
+
+    for file in ttl_files:
+        error_messages = []
+
+        log.info(f"Parse: {file}")
+        try:
+            file_graph = Graph().parse(file)
+        except BadSyntax as e:
+            template = "An exception of type {0} occurred when trying to parse a spec file. Arguments:\n{1!r}"
+            message = template.format(type(e).__name__, e.args)
+            log.error(message)
+            error_messages += [f"Could not extract spec from {file} due to exception of type "
+                               f"{type(e).__name__} when parsing file"]
+            continue
+        # run shacl validation
+        conforms, results_graph, results_text = validate(file_graph,
+                                                         shacl_graph=shacl_graph,
+                                                         ont_graph=ont_graph,
+                                                         inference='none',
+                                                         abort_on_first=False,
+                                                         allow_infos=False,
+                                                         allow_warnings=False,
+                                                         meta_shacl=False,
+                                                         advanced=True,
+                                                         js=False,
+                                                         debug=False)
+        if not conforms:
+            for msg in results_graph.objects(predicate=SH.resultMessage):
+                log.warning(f"{file_graph}")
+                log.warning(f"{msg} File: {file.name}")
+                error_messages += [f"{msg} File: {file.name}"]
+
+        # collect a list of uris of the tests in focus
+        for focus_uri in file_graph.subjects(predicate=MUST.focus, object=Literal("true", datatype=XSD.boolean)):
+            if focus_uri in focus_uris:
+                focus_uri = URIRef(str(focus_uri) + "_DUPLICATE")
+            focus_uris.add(focus_uri)
+
+        # make sure there are no duplicate test IRIs in the files
+        for subject_uri in file_graph.subjects(RDF.type, MUST.TestSpec):
+            if subject_uri in subject_uris:
+                log.warning(f"Duplicate subject URI found: {file.name} {subject_uri}. File will not be parsed.")
+                error_messages += [f"Duplicate subject URI found in {file.name}."]
+                subject_uri = URIRef(str(subject_uri) + "_DUPLICATE")
+            if len(error_messages) > 0:
+                error_messages.sort()
+                error_message = "\n".join(msg for msg in error_messages)
+                invalid_specs += [SpecSkipped(subject_uri, triple_store["type"], error_message, file.name) for triple_store in
+                                triple_stores]
+            else:
+                subject_uris.add(subject_uri)
+                this_spec_graph = Graph()
+                this_spec_graph.parse(file)
+                spec_uris_in_this_file = list(this_spec_graph.subjects(RDF.type, MUST.TestSpec))
+                for spec in spec_uris_in_this_file:
+                    # print(f"adding {tripleToAdd}")
+                    this_spec_graph.add([spec, MUST.specSourceFile, Literal(file)])
+                    this_spec_graph.add([spec, MUST.specFileName, Literal(file.name)])
+                # print(f"beforeadd: {spec_graph}" )
+                # print(f"beforeadd: {str(this_spec_graph.serialize())}" )
+                spec_graph += this_spec_graph
+
+
+    sourceFiles = list(spec_graph.subject_objects(MUST.specSourceFile))
+    # print(f"sourceFiles: {sourceFiles}")
+
+    valid_spec_uris = list(spec_graph.subjects(RDF.type, MUST.TestSpec))
+
+    if focus_uris:
+        invalid_focus_specs = []
+        for spec in invalid_specs:
+            if spec.spec_uri in focus_uris:
+                invalid_focus_specs += [spec]
+                focus_uris.remove(spec.spec_uri)
+        log.info(f"Collected {len(focus_uris)} focus test spec(s)")
+        return focus_uris, spec_graph, invalid_focus_specs
+    else:
+        log.info(f"Collected {len(valid_spec_uris)} valid test spec(s)")   
+        return valid_spec_uris, spec_graph, invalid_specs
+
+
+def get_specs(spec_uris: List[URIRef], spec_graph: Graph, triple_stores: List[dict],
+              run_config: dict):
+    specs = []
+    skipped_results = []
+    try:
+        for triple_store in triple_stores:
+            if "error" in triple_store:
+                log.error(f"{triple_store['error']}. No specs run for this triple store.")
+                skipped_results += [SpecSkipped(spec_uri, triple_store['type'], triple_store['error'], get_spec_file(spec_uri, spec_graph)) for spec_uri in
+                                    spec_uris]
+            else:
+                for spec_uri in spec_uris:
+                    try:
+                        specs += [get_spec(spec_uri, spec_graph, run_config, triple_store)]
+                    except (ValueError, FileNotFoundError, ConnectionError) as e:
+                        skipped_results += [SpecSkipped(spec_uri, triple_store['type'], e, get_spec_file(spec_uri, spec_graph))]
+
+    except (BadSyntax, FileNotFoundError) as e:
+        template = "An exception of type {0} occurred when trying to parse the triple store configuration file. " \
+                   "Arguments:\n{1!r}"
+        message = template.format(type(e).__name__, e.args)
+        log.error(message)
+        log.error("No specifications will be run.")
+
+    log.info(f"Extracted {len(specs)} specifications that will be run")
+    return specs, skipped_results
+
+
+def run_specs(specs) -> List[SpecResult]:
+    results = []
+    # https://github.com/Semantic-partners/mustrd/issues/115
+    for specification in specs:
+        results.append(run_spec(specification))
+    return results
+
+def get_spec_file(spec_uri: URIRef, spec_graph: Graph):
+    return str(spec_graph.value(subject = spec_uri, predicate = MUST.specFileName, default = "default.mustrd.ttl"))
+
+def get_spec(spec_uri: URIRef, spec_graph: Graph, run_config: dict, mustrd_triple_store: dict = None) -> Specification:
+    try:
+        if mustrd_triple_store is None:
+            mustrd_triple_store = {"type": TRIPLESTORE.RdfLib}
+        components = []
+        for predicate in MUST.given, MUST.when, MUST.then:
+            components.append(parse_spec_component(subject=spec_uri,
+                                                predicate=predicate,
+                                                spec_graph=spec_graph,
+                                                run_config=run_config,
+                                                mustrd_triple_store=mustrd_triple_store))
+
+        spec_file_name = get_spec_file(spec_uri, spec_graph)
+        # https://github.com/Semantic-partners/mustrd/issues/92
+        return Specification(spec_uri, mustrd_triple_store, components[0].value, components[1], components[2], spec_file_name)
+    
+    except (ValueError, FileNotFoundError) as e:
+        template = "An exception of type {0} occurred. Arguments:\n{1!r}"
+        message = template.format(type(e).__name__, e.args)
+        log.exception(message)
+        raise
+    except ConnectionError as e:
+        log.error(e)
+        raise
+
+
+def check_result(spec, result):
+    if type(spec.then) == TableThenSpec:
+        return table_comparison(result, spec)
+    else:
+        graph_compare = graph_comparison(spec.then.value, result)
+        if isomorphic(result, spec.then.value):
+            return SpecPassed(spec.spec_uri, spec.triple_store["type"])
+        else:
+            if spec.when[0].queryType == MUST.ConstructSparql:
+                return ConstructSpecFailure(spec.spec_uri, spec.triple_store["type"], graph_compare)
+            else:
+                return UpdateSpecFailure(spec.spec_uri, spec.triple_store["type"], graph_compare)
+
+
+def run_spec(spec: Specification) -> SpecResult:
+    spec_uri = spec.spec_uri
+    triple_store = spec.triple_store
+    # close_connection = True
+    log.debug(f"run_when {spec_uri=}, {triple_store=}, {spec.given=}, {spec.when=}, {spec.then=}")
+    if spec.given:
+        given_as_turtle = spec.given.serialize(format="turtle")
+        log.debug(f"{given_as_turtle}")
+        upload_given(triple_store, spec.given)
+    else:
+        if triple_store['type'] == TRIPLESTORE.RdfLib:
+            return SpecSkipped(spec_uri, triple_store['type'], "Unable to run Inherited State tests on Rdflib")
+    try:
+        for when in spec.when:
+            log.info(f"Running {when.queryType} spec {spec_uri} on {triple_store['type']}")
+            try:
+                result = run_when(spec_uri, triple_store, when)
+            except ParseException as e:
+                return SparqlParseFailure(spec_uri, triple_store["type"], e)
+            except NotImplementedError as ex:
+                return SpecSkipped(spec_uri, triple_store["type"], ex.args[0])
+        return check_result(spec, result)
+    except (ConnectionError, TimeoutError, HTTPError, ConnectTimeout, OSError) as e:
+        # close_connection = False
+        template = "An exception of type {0} occurred. Arguments:\n{1!r}"
+        message = template.format(type(e).__name__, e.args)
+        log.error(message)
+        return TripleStoreConnectionError(spec_uri, triple_store["type"], message)
+    except (TypeError, RequestException) as e:
+        log.error(f"{type(e)} {e}")
+        return SparqlExecutionError(spec_uri, triple_store["type"], e)
+
+    # https://github.com/Semantic-partners/mustrd/issues/78
+    # finally:
+    #     if type(mustrd_triple_store) == MustrdAnzo and close_connection:
+    #         mustrd_triple_store.clear_graph()
+
+def get_triple_store_graph(triple_store_graph_path: Path, secrets: str):
+    if secrets:
+        return Graph().parse(triple_store_graph_path).parse(data = secrets)
+    else:
+        secret_path = triple_store_graph_path.parent / Path(triple_store_graph_path.stem + "_secrets" + triple_store_graph_path.suffix)
+        return Graph().parse(triple_store_graph_path).parse(secret_path)
+    
+
+def get_triple_stores(triple_store_graph: Graph) -> list[dict]:
+    triple_stores = []
+    shacl_graph = Graph().parse(Path(os.path.join(get_mustrd_root(), "model/triplestoreshapes.ttl")))
+    ont_graph = Graph().parse(Path(os.path.join(get_mustrd_root(), "model/triplestoreOntology.ttl")))
+    conforms, results_graph, results_text = validate(
+            data_graph= triple_store_graph,
+            shacl_graph = shacl_graph,
+            ont_graph  = ont_graph,
+            advanced= True,
+            inference= 'none'
+        )
+    if not conforms:
+        raise ValueError(f"Triple store configuration not conform to the shapes. SHACL report: {results_text}", results_graph)
+    for triple_store_config, rdf_type, triple_store_type in triple_store_graph.triples((None, RDF.type, None)):
+        triple_store = {}
+        triple_store["type"] = triple_store_type
+        triple_store["uri"] = triple_store_config
+        # Anzo graph via anzo
+        if triple_store_type == TRIPLESTORE.Anzo:
+            triple_store["url"] = triple_store_graph.value(subject=triple_store_config, predicate=TRIPLESTORE.url)
+            triple_store["port"] = triple_store_graph.value(subject=triple_store_config, predicate=TRIPLESTORE.port)
+            try:
+                triple_store["username"] = str(triple_store_graph.value(subject=triple_store_config, predicate=TRIPLESTORE.username))
+                triple_store["password"] = str(triple_store_graph.value(subject=triple_store_config, predicate=TRIPLESTORE.password))
+            except (FileNotFoundError, ValueError) as e:
+                triple_store["error"] = e
+            triple_store["gqe_uri"] = triple_store_graph.value(subject=triple_store_config, predicate=TRIPLESTORE.gqeURI)
+            triple_store["input_graph"] = triple_store_graph.value(subject=triple_store_config,
+                                                                   predicate=TRIPLESTORE.inputGraph)
+            triple_store["output_graph"] = triple_store_graph.value(subject=triple_store_config,
+                                                                   predicate=TRIPLESTORE.outputGraph)
+            try:
+                check_triple_store_params(triple_store, ["url", "port", "username", "password", "input_graph"])
+            except ValueError as e:
+                triple_store["error"] = e
+        # GraphDB
+        elif triple_store_type == TRIPLESTORE.GraphDb:
+            triple_store["url"] = triple_store_graph.value(subject=triple_store_config, predicate=TRIPLESTORE.url)
+            triple_store["port"] = triple_store_graph.value(subject=triple_store_config, predicate=TRIPLESTORE.port)
+            try:
+                triple_store["username"] = str(triple_store_graph.value(subject=triple_store_config, predicate=TRIPLESTORE.username))
+                triple_store["password"] = str(triple_store_graph.value(subject=triple_store_config, predicate=TRIPLESTORE.password))
+            except (FileNotFoundError, ValueError) as e:
+                log.error(f"Credential retrieval failed {e}")
+                triple_store["error"] = e
+            triple_store["repository"] = triple_store_graph.value(subject=triple_store_config,
+                                                                  predicate=TRIPLESTORE.repository)
+            triple_store["input_graph"] = triple_store_graph.value(subject=triple_store_config,
+                                                                   predicate=TRIPLESTORE.inputGraph)
+
+            try:
+                check_triple_store_params(triple_store, ["url", "port", "repository"])
+            except ValueError as e:
+                triple_store["error"] = e
+        elif triple_store_type != TRIPLESTORE.RdfLib:
+            triple_store["error"] = f"Triple store not implemented: {triple_store_type}"
+
+        triple_stores.append(triple_store)
+    return triple_stores
+
+
+def check_triple_store_params(triple_store: dict, required_params: List[str]):
+    missing_params = [param for param in required_params if triple_store.get(param) is None]
+    if missing_params:
+        raise ValueError(f"Cannot establish connection to {triple_store['type']}. "
+                         f"Missing required parameter(s): {', '.join(missing_params)}.")
+
+
+def get_credential_from_file(triple_store_name: URIRef, credential: str, config_path: Literal) -> str:
+    log.info(f"get_credential_from_file {triple_store_name}, {credential}, {config_path}")
+    if config_path is None:
+        raise ValueError(f"Cannot establish connection defined in {triple_store_name}. "
+                         f"Missing required parameter: {credential}.")
+    # if os.path.isrelative(config_path)
+    # project_root = get_project_root()
+    path = Path(config_path)
+    log.info(f"get_credential_from_file {path}")
+
+    if not os.path.isfile(path):
+        log.error(f"couldn't find {path}")
+        raise FileNotFoundError(f"Credentials config file not found: {path}")
+    try:
+        with open(path, "rb") as f:
+            config = tomli.load(f)
+    except tomli.TOMLDecodeError as e:
+        log.error(f"config error {path} {e}")
+        raise ValueError(f"Error reading credentials config file: {e}")
+    return config[str(triple_store_name)][credential]
+
+# Convert sparql json query results as defined in https://www.w3.org/TR/rdf-sparql-json-res/
+def json_results_to_panda_dataframe(result: str) -> pandas.DataFrame:
+    json_result = json.loads(result)
+    frames = DataFrame()
+    for binding in json_result["results"]["bindings"]:
+        columns = []
+        values = []
+        for key in binding:
+            value_object = binding[key]
+            columns.append(key)
+            values.append(str(value_object["value"]))
+            columns.append(key + "_datatype")
+            if "type" in value_object and value_object["type"] == "literal":
+                literal_type = str(XSD.string)
+                if "datatype" in value_object:
+                    literal_type = value_object["datatype"]
+                values.append(literal_type)
+            else:
+                values.append(str(XSD.anyURI))
+
+        frames = pandas.concat(objs=[frames, pandas.DataFrame([values], columns=columns)], ignore_index=True)
+        frames.fillna('', inplace=True)
+
+        if frames.size == 0:
+            frames = pandas.DataFrame()
+    return frames
+
+
+# https://github.com/Semantic-partners/mustrd/issues/110
+# https://github.com/Semantic-partners/mustrd/issues/52
+def table_comparison(result: str, spec: Specification) -> SpecResult:
+    warning = None
+    order_list = ["order by ?", "order by desc", "order by asc"]
+    ordered_result = any(pattern in spec.when[0].value.lower() for pattern in order_list)
+    then = spec.then.value
+    try:
+        if is_json(result):
+            df = json_results_to_panda_dataframe(result)
+            columns = list(df.columns)
+        else:
+            raise ParseException
+        sorted_columns = sorted(columns)
+        sorted_then_cols = sorted(list(then))
+        if not df.empty:
+
+            if not ordered_result:
+                df.sort_values(by=columns[::2], inplace=True)
+                df.reset_index(inplace=True, drop=True)
+                if spec.then.ordered:
+                    warning = f"sh:order in {spec.spec_uri} is ignored, no ORDER BY in query"
+                    log.warning(warning)
+
+            # Scenario 1: expected no result but got a result
+            if then.empty:
+                message = f"Expected 0 row(s) and 0 column(s), got {df.shape[0]} row(s) and {round(df.shape[1] / 2)} column(s)"
+                empty_then = create_empty_dataframe_with_columns(df)
+                df_diff = empty_then.compare(df, result_names=("expected", "actual"))
+
+            else:
+                # Scenario 2: expected a result and got a result
+                # pandas.set_option('display.max_columns', None)
+                message = f"Expected {then.shape[0]} row(s) and {round(then.shape[1] / 2)} column(s), " \
+                          f"got {df.shape[0]} row(s) and {round(df.shape[1] / 2)} column(s)"
+                if ordered_result is True and not spec.then.ordered:
+                    message += ". Actual result is ordered, must:then must contain sh:order on every row."
+                    return SelectSpecFailure(spec.spec_uri, spec.triple_store["type"], None, message)
+                    # if df.shape == then.shape and (df.columns == then.columns).all():
+                    #     df_diff = then.compare(df, result_names=("expected", "actual"))
+                    #     if df_diff.empty:
+                    #         df_diff = df
+                    #         print(df_diff.to_markdown())
+                    # else:
+                    #     df_diff = construct_df_diff(df, then)
+                    #     print(df_diff.to_markdown())
+                else:
+                    if len(columns) == len(then.columns):
+                        if sorted_columns == sorted_then_cols:
+                            then = then[columns]
+                            if not ordered_result:
+                                then.sort_values(by=columns[::2], inplace=True)
+                                then.reset_index(drop=True, inplace=True)
+                            if df.shape == then.shape and (df.columns == then.columns).all():
+                                df_diff = then.compare(df, result_names=("expected", "actual"))
+                            else:
+                                df_diff = construct_df_diff(df, then)
+
+                        else:
+                            then = then[sorted_then_cols]
+                            df = df[sorted_columns]
+                            df_diff = construct_df_diff(df, then)
+                    else:
+
+                        then = then[sorted_then_cols]
+                        df = df[sorted_columns]
+                        df_diff = construct_df_diff(df, then)
+        else:
+
+            if then.empty:
+                # Scenario 3: expected no result, got no result
+                message = f"Expected 0 row(s) and 0 column(s), got 0 row(s) and 0 column(s)"
+                df = pandas.DataFrame()
+            else:
+                # Scenario 4: expected a result, but got an empty result
+                message = f"Expected {then.shape[0]} row(s) and {round(then.shape[1] / 2)} column(s), got 0 row(s) and 0 column(s)"
+                then = then[sorted_then_cols]
+                df = create_empty_dataframe_with_columns(then)
+            df_diff = then.compare(df, result_names=("expected", "actual"))
+            print(df_diff.to_markdown())
+
+        if df_diff.empty:
+            if warning:
+                return SpecPassedWithWarning(spec.spec_uri, spec.triple_store["type"], warning)
+            else:
+                return SpecPassed(spec.spec_uri, spec.triple_store["type"])
+        else:
+            # message += f"\nexpected:\n{then}\nactual:{df}"
+            log.error(message)
+            # print(spec.spec_uri)
+            # print("actual:")
+            # print(then)
+            # print("expected:")
+            # print(df)
+            return SelectSpecFailure(spec.spec_uri, spec.triple_store["type"], df_diff, message)
+
+    except ParseException as e:
+        return SparqlParseFailure(spec.spec_uri, spec.triple_store["type"], e)
+    except NotImplementedError as ex:
+        return SpecSkipped(spec.spec_uri, spec.triple_store["type"], ex)
+
+
+def graph_comparison(expected_graph: Graph, actual_graph: Graph) -> GraphComparison:
+    diff = graph_diff(expected_graph, actual_graph)
+    in_both = diff[0]
+    in_expected = diff[1]
+    in_actual = diff[2]
+    in_expected_not_in_actual = (in_expected - in_actual)
+    in_actual_not_in_expected = (in_actual - in_expected)
+    return GraphComparison(in_expected_not_in_actual, in_actual_not_in_expected, in_both)
+
+
+def get_then_update(spec_uri: URIRef, spec_graph: Graph) -> Graph:
+    then_query = f"""
+    prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> 
+
+    CONSTRUCT {{ ?s ?p ?o }}
+    {{
+        <{spec_uri}> <{MUST.then}> 
+            a <{MUST.StatementsDataset}> ;
+            <{MUST.hasStatement}> [
+                a rdf:Statement ;
+                rdf:subject ?s ;
+                rdf:predicate ?p ;
+                rdf:object ?o ;
+            ] ; ] 
+    }}
+    """
+    expected_results = spec_graph.query(then_query).graph
+
+    return expected_results
+
+
+def calculate_row_difference(df1: pandas.DataFrame,
+                             df2: pandas.DataFrame) -> pandas.DataFrame:
+    df_all = df1.merge(df2.drop_duplicates(), how='left', indicator=True)
+    actual_rows = df_all[df_all['_merge'] == 'left_only']
+    actual_rows = actual_rows.drop('_merge', axis=1)
+    return actual_rows
+
+
+def construct_df_diff(df: pandas.DataFrame,
+                      then: pandas.DataFrame) -> pandas.DataFrame:
+    actual_rows = calculate_row_difference(df, then)
+    expected_rows = calculate_row_difference(then, df)
+    actual_columns = df.columns.difference(then.columns)
+    expected_columns = then.columns.difference(df.columns)
+
+    df_diff = pandas.DataFrame()
+    modified_df = df
+    modified_then = then
+
+    if actual_columns.size > 0:
+        modified_then = modified_then.reindex(modified_then.columns.to_list() + actual_columns.to_list(), axis=1)
+        modified_then[actual_columns.to_list()] = modified_then[actual_columns.to_list()].fillna('')
+
+    if expected_columns.size > 0:
+        modified_df = modified_df.reindex(modified_df.columns.to_list() + expected_columns.to_list(), axis=1)
+        modified_df[expected_columns.to_list()] = modified_df[expected_columns.to_list()].fillna('')
+
+    modified_df = modified_df.reindex(modified_then.columns, axis=1)
+
+    if df.shape[0] != then.shape[0] and df.shape[1] != then.shape[1]:
+        # take modified columns and add rows
+        actual_rows = calculate_row_difference(modified_df, modified_then)
+        expected_rows = calculate_row_difference(modified_then, modified_df)
+        df_diff = generate_row_diff(actual_rows, expected_rows)
+    elif actual_rows.shape[0] > 0 or expected_rows.shape[0] > 0:
+        df_diff = generate_row_diff(actual_rows, expected_rows)
+    elif actual_columns.size > 0 or expected_columns.size > 0:
+        df_diff = modified_then.compare(modified_df, result_names=("expected", "actual"), keep_shape=True,
+                                        keep_equal=True)
+    df_diff.fillna("", inplace=True)
+    return df_diff
+
+
+def generate_row_diff(actual_rows: pandas.DataFrame, expected_rows: pandas.DataFrame) -> pandas.DataFrame:
+    df_diff_actual_rows = pandas.DataFrame()
+    df_diff_expected_rows = pandas.DataFrame()
+
+    if actual_rows.shape[0] > 0:
+        empty_actual_copy = create_empty_dataframe_with_columns(actual_rows)
+        df_diff_actual_rows = empty_actual_copy.compare(actual_rows, result_names=("expected", "actual"))
+
+    if expected_rows.shape[0] > 0:
+        empty_expected_copy = create_empty_dataframe_with_columns(expected_rows)
+        df_diff_expected_rows = expected_rows.compare(empty_expected_copy, result_names=("expected", "actual"))
+
+    df_diff_rows = pandas.concat([df_diff_actual_rows, df_diff_expected_rows], ignore_index=True)
+    return df_diff_rows
+
+
+def create_empty_dataframe_with_columns(df: pandas.DataFrame) -> pandas.DataFrame:
+    empty_copy = pandas.DataFrame().reindex_like(df)
+    empty_copy.fillna("", inplace=True)
+    return empty_copy
+
+
+def review_results(results: List[SpecResult], verbose: bool) -> None:
+    print("===== Result Overview =====")
+    # Init dictionaries
+    status_dict = defaultdict(lambda: defaultdict(int))
+    status_counts = defaultdict(lambda: defaultdict(int))
+    colours = {SpecPassed: Fore.GREEN, SpecPassedWithWarning: Fore.YELLOW, SpecSkipped: Fore.YELLOW}
+    # Populate dictionaries from results
+    for result in results:
+        status_counts[result.triple_store][type(result)] += 1
+        status_dict[result.spec_uri][result.triple_store] = type(result)
+
+    # Get the list of statuses and list of unique triple stores
+    statuses = list(status for inner_dict in status_dict.values() for status in inner_dict.values())
+    triple_stores = list(set(status for inner_dict in status_dict.values() for status in inner_dict.keys()))
+
+    # Convert dictionaries to list for tabulate
+    table_rows = [[spec_uri] + [
+        f"{colours.get(status_dict[spec_uri][triple_store], Fore.RED)}{status_dict[spec_uri][triple_store].__name__}{Style.RESET_ALL}"
+        for triple_store in triple_stores] for spec_uri in set(status_dict.keys())]
+
+    status_rows = [[f"{colours.get(status, Fore.RED)}{status.__name__}{Style.RESET_ALL}"] +
+                   [f"{colours.get(status, Fore.RED)}{status_counts[triple_store][status]}{Style.RESET_ALL}"
+                    for triple_store in triple_stores] for status in set(statuses)]
+
+    # Display tables with tabulate
+    print(tabulate(table_rows, headers=['Spec Uris / triple stores'] + triple_stores, tablefmt="pretty"))
+    print(tabulate(status_rows, headers=['Status / triple stores'] + triple_stores, tablefmt="pretty"))
+
+    pass_count = statuses.count(SpecPassed)
+    warning_count = statuses.count(SpecPassedWithWarning)
+    skipped_count = statuses.count(SpecSkipped)
+    fail_count = len(
+        list(filter(lambda status: status not in [SpecPassed, SpecPassedWithWarning, SpecSkipped], statuses)))
+
+    if fail_count:
+        overview_colour = Fore.RED
+    elif warning_count or skipped_count:
+        overview_colour = Fore.YELLOW
+    else:
+        overview_colour = Fore.GREEN
+
+    logger_setup.flush()
+    print(f"{overview_colour}===== {fail_count} failures, {skipped_count} skipped, {Fore.GREEN}{pass_count} passed, "
+          f"{overview_colour}{warning_count} passed with warnings =====")
+
+    if verbose and (fail_count or warning_count or skipped_count):
+        for res in results:
+            if type(res) == UpdateSpecFailure:
+                print(f"{Fore.RED}Failed {res.spec_uri} {res.triple_store}")
+                print(f"{Fore.BLUE} In Expected Not In Actual:")
+                print(res.graph_comparison.in_expected_not_in_actual.serialize(format="ttl"))
+                print()
+                print(f"{Fore.RED} in_actual_not_in_expected")
+                print(res.graph_comparison.in_actual_not_in_expected.serialize(format="ttl"))
+                print(f"{Fore.GREEN} in_both")
+                print(res.graph_comparison.in_both.serialize(format="ttl"))
+
+            if type(res) == SelectSpecFailure:
+                print(f"{Fore.RED}Failed {res.spec_uri} {res.triple_store}")
+                print(res.message)
+                print(res.table_comparison.to_markdown())
+            if type(res) == ConstructSpecFailure or type(res) == UpdateSpecFailure:
+                print(f"{Fore.RED}Failed {res.spec_uri} {res.triple_store}")
+            if type(res) == SpecPassedWithWarning:
+                print(f"{Fore.YELLOW}Passed with warning {res.spec_uri} {res.triple_store}")
+                print(res.warning)
+            if type(res) == TripleStoreConnectionError or type(res) == SparqlExecutionError or \
+                    type(res) == SparqlParseFailure:
+                print(f"{Fore.RED}Failed {res.spec_uri} {res.triple_store}")
+                print(res.exception)
+            if type(res) == SpecSkipped:
+                print(f"{Fore.YELLOW}Skipped {res.spec_uri} {res.triple_store}")
+                print(res.message)
+
+
+
+    
+
+