haystack/test/document_stores/test_knowledge_graph.py

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knowledge graph example (#934) * Add knowledge graph module * Fix type hint * Add graph retriver module * Change type annotations, change return format * Add graph retriever that executes questions as sparql queries * Linking only those entities that are in the knowledge graph * Added logging and using relations extracted from Knowledge graph for linking * Preventing entity linking from linking the same token to multiple entities * Pruning triples that have no variables for select and count queries * Support knowledge graphs with Pipelines * Add text2sparql * Entity linking and relation linking consider more special cases now based on evaluation on labelled data * Separating example code from KGQA implementation * Add eval on combined extarctive and kg questions * Remove references to hp-test * Add fields sparql_query and long_answer_list to metadata * Removing modular Question2SPARQL approach * Removing additional classes used for modular kgqa approach * preparing lcquad data * change graph db * Translating namespaces in knowledge graph queries * Creating graphdb index and loading triples from .ttl file * Fetching graph config files, triples and model from S3 * Fix incompatibility issues with BaseGraphRetriever and BaseComponent * Removing unused utility functions * Adding doc strings and tutorial header * Adding sparqlwrapper dependency * Moving tutorial header * Sorting tutorials by number within name of notebook * Add latest docstring and tutorial changes * Creating test cases for knowledge graph * Changing knowledge graph example to harry potter * Add latest docstring and tutorial changes * Adapting the tutorial notebook to harry potter example * Add GraphDB fixture for tests * Add latest docstring and tutorial changes * Added GraphDB docker launch to CI * Use correct GraphDB fixture * Check if GraphDB instance is already running * Renaming question/query and incorporating other feedback from Timo and Tanay * Removed type annotation * Add latest docstring and tutorial changes Co-authored-by: oryx1729 <oryx1729@protonmail.com> Co-authored-by: Timo Moeller <timo.moeller@deepset.ai> Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>
2021-04-08 14:05:33 +02:00
from pathlib import Path
import pytest
Refactoring of the `haystack` package (#1624) * Files moved, imports all broken * Fix most imports and docstrings into * Fix the paths to the modules in the API docs * Add latest docstring and tutorial changes * Add a few pipelines that were lost in the inports * Fix a bunch of mypy warnings * Add latest docstring and tutorial changes * Create a file_classifier module * Add docs for file_classifier * Fixed most circular imports, now the REST API can start * Add latest docstring and tutorial changes * Tackling more mypy issues * Reintroduce from FARM and fix last mypy issues hopefully * Re-enable old-style imports * Fix some more import from the top-level package in an attempt to sort out circular imports * Fix some imports in tests to new-style to prevent failed class equalities from breaking tests * Change document_store into document_stores * Update imports in tutorials * Add latest docstring and tutorial changes * Probably fixes summarizer tests * Improve the old-style import allowing module imports (should work) * Try to fix the docs * Remove dedicated KnowledgeGraph page from autodocs * Remove dedicated GraphRetriever page from autodocs * Fix generate_docstrings.sh with an updated list of yaml files to look for * Fix some more modules in the docs * Fix the document stores docs too * Fix a small issue on Tutorial14 * Add latest docstring and tutorial changes * Add deprecation warning to old-style imports * Remove stray folder and import Dict into dense.py * Change import path for MLFlowLogger * Add old loggers path to the import path aliases * Fix debug output of convert_ipynb.py * Fix circular import on BaseRetriever * Missed one merge block * re-run tutorial 5 * Fix imports in tutorial 5 * Re-enable squad_to_dpr CLI from the root package and move get_batches_from_generator into document_stores.base * Add latest docstring and tutorial changes * Fix typo in utils __init__ * Fix a few more imports * Fix benchmarks too * New-style imports in test_knowledge_graph * Rollback setup.py * Rollback squad_to_dpr too Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>
2021-10-25 15:50:23 +02:00
from haystack.nodes import Text2SparqlRetriever
from haystack.document_stores import GraphDBKnowledgeGraph
from haystack.utils import fetch_archive_from_http
knowledge graph example (#934) * Add knowledge graph module * Fix type hint * Add graph retriver module * Change type annotations, change return format * Add graph retriever that executes questions as sparql queries * Linking only those entities that are in the knowledge graph * Added logging and using relations extracted from Knowledge graph for linking * Preventing entity linking from linking the same token to multiple entities * Pruning triples that have no variables for select and count queries * Support knowledge graphs with Pipelines * Add text2sparql * Entity linking and relation linking consider more special cases now based on evaluation on labelled data * Separating example code from KGQA implementation * Add eval on combined extarctive and kg questions * Remove references to hp-test * Add fields sparql_query and long_answer_list to metadata * Removing modular Question2SPARQL approach * Removing additional classes used for modular kgqa approach * preparing lcquad data * change graph db * Translating namespaces in knowledge graph queries * Creating graphdb index and loading triples from .ttl file * Fetching graph config files, triples and model from S3 * Fix incompatibility issues with BaseGraphRetriever and BaseComponent * Removing unused utility functions * Adding doc strings and tutorial header * Adding sparqlwrapper dependency * Moving tutorial header * Sorting tutorials by number within name of notebook * Add latest docstring and tutorial changes * Creating test cases for knowledge graph * Changing knowledge graph example to harry potter * Add latest docstring and tutorial changes * Adapting the tutorial notebook to harry potter example * Add GraphDB fixture for tests * Add latest docstring and tutorial changes * Added GraphDB docker launch to CI * Use correct GraphDB fixture * Check if GraphDB instance is already running * Renaming question/query and incorporating other feedback from Timo and Tanay * Removed type annotation * Add latest docstring and tutorial changes Co-authored-by: oryx1729 <oryx1729@protonmail.com> Co-authored-by: Timo Moeller <timo.moeller@deepset.ai> Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>
2021-04-08 14:05:33 +02:00
Add CI for windows runner (#1458) * Feat: Removing use of temp file while downloading archive from url along with adding CI for windows and mac platform * Windows CI by default installing pytorch gpu hence updating CI to pick cpu version * fixing mac cache build issue * updating windows pip install command for torch * another attempt * updating ci * Adding sudo * fixing ls failure on windows * another attempt to fix build issue * Saving env variable of test files * Adding debug log * Github action differ on windows * adding debug * anohter attempt * Windows have different ways to receive env * fixing template * minor fx * Adding debug * Removing use of json * Adding back fromJson * addin toJson * removing print * anohter attempt * disabling parallel run at least for testing * installing docker for mac runner * correcting docker install command * Linux dockers are not suported in windows * Removing mac changes * Upgrading pytorch * using lts pytorch * Separating win and ubuntu * Install java 11 * enabling linux container env * docker cli command * docker cli command * start elastic service * List all service * correcting service name * Attempt to fix multiple test run * convert to json * another attempt to check * Updating build cache step * attempt * Add tika * Separating windows CI * Changing CI name * Skipping test which does not work in windows * Skipping tests for windows * create cleanup function in conftest * adding skipif marker on tests * Run windows PR on only push to master * Addressing review comments * Enabling windows ci for this PR * Tika init is being called when importing tika function * handling tika import issue * handling tika import issue in test * Fixing import issue * removing tika fixure * Removing fixture from tests * Disable windows ci on pull request * Add back extra pytorch install step Co-authored-by: Malte Pietsch <malte.pietsch@deepset.ai>
2021-10-29 13:52:28 +05:30
knowledge graph example (#934) * Add knowledge graph module * Fix type hint * Add graph retriver module * Change type annotations, change return format * Add graph retriever that executes questions as sparql queries * Linking only those entities that are in the knowledge graph * Added logging and using relations extracted from Knowledge graph for linking * Preventing entity linking from linking the same token to multiple entities * Pruning triples that have no variables for select and count queries * Support knowledge graphs with Pipelines * Add text2sparql * Entity linking and relation linking consider more special cases now based on evaluation on labelled data * Separating example code from KGQA implementation * Add eval on combined extarctive and kg questions * Remove references to hp-test * Add fields sparql_query and long_answer_list to metadata * Removing modular Question2SPARQL approach * Removing additional classes used for modular kgqa approach * preparing lcquad data * change graph db * Translating namespaces in knowledge graph queries * Creating graphdb index and loading triples from .ttl file * Fetching graph config files, triples and model from S3 * Fix incompatibility issues with BaseGraphRetriever and BaseComponent * Removing unused utility functions * Adding doc strings and tutorial header * Adding sparqlwrapper dependency * Moving tutorial header * Sorting tutorials by number within name of notebook * Add latest docstring and tutorial changes * Creating test cases for knowledge graph * Changing knowledge graph example to harry potter * Add latest docstring and tutorial changes * Adapting the tutorial notebook to harry potter example * Add GraphDB fixture for tests * Add latest docstring and tutorial changes * Added GraphDB docker launch to CI * Use correct GraphDB fixture * Check if GraphDB instance is already running * Renaming question/query and incorporating other feedback from Timo and Tanay * Removed type annotation * Add latest docstring and tutorial changes Co-authored-by: oryx1729 <oryx1729@protonmail.com> Co-authored-by: Timo Moeller <timo.moeller@deepset.ai> Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>
2021-04-08 14:05:33 +02:00
@pytest.mark.graphdb
Add CI for windows runner (#1458) * Feat: Removing use of temp file while downloading archive from url along with adding CI for windows and mac platform * Windows CI by default installing pytorch gpu hence updating CI to pick cpu version * fixing mac cache build issue * updating windows pip install command for torch * another attempt * updating ci * Adding sudo * fixing ls failure on windows * another attempt to fix build issue * Saving env variable of test files * Adding debug log * Github action differ on windows * adding debug * anohter attempt * Windows have different ways to receive env * fixing template * minor fx * Adding debug * Removing use of json * Adding back fromJson * addin toJson * removing print * anohter attempt * disabling parallel run at least for testing * installing docker for mac runner * correcting docker install command * Linux dockers are not suported in windows * Removing mac changes * Upgrading pytorch * using lts pytorch * Separating win and ubuntu * Install java 11 * enabling linux container env * docker cli command * docker cli command * start elastic service * List all service * correcting service name * Attempt to fix multiple test run * convert to json * another attempt to check * Updating build cache step * attempt * Add tika * Separating windows CI * Changing CI name * Skipping test which does not work in windows * Skipping tests for windows * create cleanup function in conftest * adding skipif marker on tests * Run windows PR on only push to master * Addressing review comments * Enabling windows ci for this PR * Tika init is being called when importing tika function * handling tika import issue * handling tika import issue in test * Fixing import issue * removing tika fixure * Removing fixture from tests * Disable windows ci on pull request * Add back extra pytorch install step Co-authored-by: Malte Pietsch <malte.pietsch@deepset.ai>
2021-10-29 13:52:28 +05:30
def test_graph_retrieval():
knowledge graph example (#934) * Add knowledge graph module * Fix type hint * Add graph retriver module * Change type annotations, change return format * Add graph retriever that executes questions as sparql queries * Linking only those entities that are in the knowledge graph * Added logging and using relations extracted from Knowledge graph for linking * Preventing entity linking from linking the same token to multiple entities * Pruning triples that have no variables for select and count queries * Support knowledge graphs with Pipelines * Add text2sparql * Entity linking and relation linking consider more special cases now based on evaluation on labelled data * Separating example code from KGQA implementation * Add eval on combined extarctive and kg questions * Remove references to hp-test * Add fields sparql_query and long_answer_list to metadata * Removing modular Question2SPARQL approach * Removing additional classes used for modular kgqa approach * preparing lcquad data * change graph db * Translating namespaces in knowledge graph queries * Creating graphdb index and loading triples from .ttl file * Fetching graph config files, triples and model from S3 * Fix incompatibility issues with BaseGraphRetriever and BaseComponent * Removing unused utility functions * Adding doc strings and tutorial header * Adding sparqlwrapper dependency * Moving tutorial header * Sorting tutorials by number within name of notebook * Add latest docstring and tutorial changes * Creating test cases for knowledge graph * Changing knowledge graph example to harry potter * Add latest docstring and tutorial changes * Adapting the tutorial notebook to harry potter example * Add GraphDB fixture for tests * Add latest docstring and tutorial changes * Added GraphDB docker launch to CI * Use correct GraphDB fixture * Check if GraphDB instance is already running * Renaming question/query and incorporating other feedback from Timo and Tanay * Removed type annotation * Add latest docstring and tutorial changes Co-authored-by: oryx1729 <oryx1729@protonmail.com> Co-authored-by: Timo Moeller <timo.moeller@deepset.ai> Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>
2021-04-08 14:05:33 +02:00
# TODO rename doc_dir
graph_dir = "../data/tutorial10_knowledge_graph/"
s3_url = "https://fandom-qa.s3-eu-west-1.amazonaws.com/triples_and_config.zip"
fetch_archive_from_http(url=s3_url, output_dir=graph_dir)
# Fetch a pre-trained BART model that translates natural language questions to SPARQL queries
model_dir = "../saved_models/tutorial10_knowledge_graph/"
s3_url = "https://fandom-qa.s3-eu-west-1.amazonaws.com/saved_models/hp_v3.4.zip"
fetch_archive_from_http(url=s3_url, output_dir=model_dir)
kg = GraphDBKnowledgeGraph(index="tutorial_10_index")
kg.delete_index()
kg.create_index(config_path=Path(graph_dir + "repo-config.ttl"))
kg.import_from_ttl_file(index="tutorial_10_index", path=Path(graph_dir + "triples.ttl"))
triple = {
"p": {"type": "uri", "value": "https://deepset.ai/harry_potter/_paternalgrandfather"},
"s": {"type": "uri", "value": "https://deepset.ai/harry_potter/Melody_fawley"},
"o": {"type": "uri", "value": "https://deepset.ai/harry_potter/Marshall_fawley"},
}
knowledge graph example (#934) * Add knowledge graph module * Fix type hint * Add graph retriver module * Change type annotations, change return format * Add graph retriever that executes questions as sparql queries * Linking only those entities that are in the knowledge graph * Added logging and using relations extracted from Knowledge graph for linking * Preventing entity linking from linking the same token to multiple entities * Pruning triples that have no variables for select and count queries * Support knowledge graphs with Pipelines * Add text2sparql * Entity linking and relation linking consider more special cases now based on evaluation on labelled data * Separating example code from KGQA implementation * Add eval on combined extarctive and kg questions * Remove references to hp-test * Add fields sparql_query and long_answer_list to metadata * Removing modular Question2SPARQL approach * Removing additional classes used for modular kgqa approach * preparing lcquad data * change graph db * Translating namespaces in knowledge graph queries * Creating graphdb index and loading triples from .ttl file * Fetching graph config files, triples and model from S3 * Fix incompatibility issues with BaseGraphRetriever and BaseComponent * Removing unused utility functions * Adding doc strings and tutorial header * Adding sparqlwrapper dependency * Moving tutorial header * Sorting tutorials by number within name of notebook * Add latest docstring and tutorial changes * Creating test cases for knowledge graph * Changing knowledge graph example to harry potter * Add latest docstring and tutorial changes * Adapting the tutorial notebook to harry potter example * Add GraphDB fixture for tests * Add latest docstring and tutorial changes * Added GraphDB docker launch to CI * Use correct GraphDB fixture * Check if GraphDB instance is already running * Renaming question/query and incorporating other feedback from Timo and Tanay * Removed type annotation * Add latest docstring and tutorial changes Co-authored-by: oryx1729 <oryx1729@protonmail.com> Co-authored-by: Timo Moeller <timo.moeller@deepset.ai> Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>
2021-04-08 14:05:33 +02:00
triples = kg.get_all_triples()
assert len(triples) > 0
assert triple in triples
# Define prefixes for names of resources so that we can use shorter resource names in queries
prefixes = """PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
PREFIX xsd: <http://www.w3.org/2001/XMLSchema#>
PREFIX hp: <https://deepset.ai/harry_potter/>
"""
kg.prefixes = prefixes
kgqa_retriever = Text2SparqlRetriever(knowledge_graph=kg, model_name_or_path=model_dir + "hp_v3.4")
knowledge graph example (#934) * Add knowledge graph module * Fix type hint * Add graph retriver module * Change type annotations, change return format * Add graph retriever that executes questions as sparql queries * Linking only those entities that are in the knowledge graph * Added logging and using relations extracted from Knowledge graph for linking * Preventing entity linking from linking the same token to multiple entities * Pruning triples that have no variables for select and count queries * Support knowledge graphs with Pipelines * Add text2sparql * Entity linking and relation linking consider more special cases now based on evaluation on labelled data * Separating example code from KGQA implementation * Add eval on combined extarctive and kg questions * Remove references to hp-test * Add fields sparql_query and long_answer_list to metadata * Removing modular Question2SPARQL approach * Removing additional classes used for modular kgqa approach * preparing lcquad data * change graph db * Translating namespaces in knowledge graph queries * Creating graphdb index and loading triples from .ttl file * Fetching graph config files, triples and model from S3 * Fix incompatibility issues with BaseGraphRetriever and BaseComponent * Removing unused utility functions * Adding doc strings and tutorial header * Adding sparqlwrapper dependency * Moving tutorial header * Sorting tutorials by number within name of notebook * Add latest docstring and tutorial changes * Creating test cases for knowledge graph * Changing knowledge graph example to harry potter * Add latest docstring and tutorial changes * Adapting the tutorial notebook to harry potter example * Add GraphDB fixture for tests * Add latest docstring and tutorial changes * Added GraphDB docker launch to CI * Use correct GraphDB fixture * Check if GraphDB instance is already running * Renaming question/query and incorporating other feedback from Timo and Tanay * Removed type annotation * Add latest docstring and tutorial changes Co-authored-by: oryx1729 <oryx1729@protonmail.com> Co-authored-by: Timo Moeller <timo.moeller@deepset.ai> Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>
2021-04-08 14:05:33 +02:00
result = kgqa_retriever.retrieve(query="In which house is Harry Potter?")
assert result[0] == {
"answer": ["https://deepset.ai/harry_potter/Gryffindor"],
"prediction_meta": {
"model": "Text2SparqlRetriever",
"sparql_query": "select ?a { hp:Harry_potter hp:house ?a . }",
},
}
knowledge graph example (#934) * Add knowledge graph module * Fix type hint * Add graph retriver module * Change type annotations, change return format * Add graph retriever that executes questions as sparql queries * Linking only those entities that are in the knowledge graph * Added logging and using relations extracted from Knowledge graph for linking * Preventing entity linking from linking the same token to multiple entities * Pruning triples that have no variables for select and count queries * Support knowledge graphs with Pipelines * Add text2sparql * Entity linking and relation linking consider more special cases now based on evaluation on labelled data * Separating example code from KGQA implementation * Add eval on combined extarctive and kg questions * Remove references to hp-test * Add fields sparql_query and long_answer_list to metadata * Removing modular Question2SPARQL approach * Removing additional classes used for modular kgqa approach * preparing lcquad data * change graph db * Translating namespaces in knowledge graph queries * Creating graphdb index and loading triples from .ttl file * Fetching graph config files, triples and model from S3 * Fix incompatibility issues with BaseGraphRetriever and BaseComponent * Removing unused utility functions * Adding doc strings and tutorial header * Adding sparqlwrapper dependency * Moving tutorial header * Sorting tutorials by number within name of notebook * Add latest docstring and tutorial changes * Creating test cases for knowledge graph * Changing knowledge graph example to harry potter * Add latest docstring and tutorial changes * Adapting the tutorial notebook to harry potter example * Add GraphDB fixture for tests * Add latest docstring and tutorial changes * Added GraphDB docker launch to CI * Use correct GraphDB fixture * Check if GraphDB instance is already running * Renaming question/query and incorporating other feedback from Timo and Tanay * Removed type annotation * Add latest docstring and tutorial changes Co-authored-by: oryx1729 <oryx1729@protonmail.com> Co-authored-by: Timo Moeller <timo.moeller@deepset.ai> Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>
2021-04-08 14:05:33 +02:00
result = kgqa_retriever._query_kg(
sparql_query="select distinct ?sbj where { ?sbj hp:job hp:Keeper_of_keys_and_grounds . }"
)
knowledge graph example (#934) * Add knowledge graph module * Fix type hint * Add graph retriver module * Change type annotations, change return format * Add graph retriever that executes questions as sparql queries * Linking only those entities that are in the knowledge graph * Added logging and using relations extracted from Knowledge graph for linking * Preventing entity linking from linking the same token to multiple entities * Pruning triples that have no variables for select and count queries * Support knowledge graphs with Pipelines * Add text2sparql * Entity linking and relation linking consider more special cases now based on evaluation on labelled data * Separating example code from KGQA implementation * Add eval on combined extarctive and kg questions * Remove references to hp-test * Add fields sparql_query and long_answer_list to metadata * Removing modular Question2SPARQL approach * Removing additional classes used for modular kgqa approach * preparing lcquad data * change graph db * Translating namespaces in knowledge graph queries * Creating graphdb index and loading triples from .ttl file * Fetching graph config files, triples and model from S3 * Fix incompatibility issues with BaseGraphRetriever and BaseComponent * Removing unused utility functions * Adding doc strings and tutorial header * Adding sparqlwrapper dependency * Moving tutorial header * Sorting tutorials by number within name of notebook * Add latest docstring and tutorial changes * Creating test cases for knowledge graph * Changing knowledge graph example to harry potter * Add latest docstring and tutorial changes * Adapting the tutorial notebook to harry potter example * Add GraphDB fixture for tests * Add latest docstring and tutorial changes * Added GraphDB docker launch to CI * Use correct GraphDB fixture * Check if GraphDB instance is already running * Renaming question/query and incorporating other feedback from Timo and Tanay * Removed type annotation * Add latest docstring and tutorial changes Co-authored-by: oryx1729 <oryx1729@protonmail.com> Co-authored-by: Timo Moeller <timo.moeller@deepset.ai> Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>
2021-04-08 14:05:33 +02:00
assert result[0][0] == "https://deepset.ai/harry_potter/Rubeus_hagrid"
result = kgqa_retriever._query_kg(
sparql_query="select distinct ?obj where { <https://deepset.ai/harry_potter/Hermione_granger> <https://deepset.ai/harry_potter/patronus> ?obj . }"
)
knowledge graph example (#934) * Add knowledge graph module * Fix type hint * Add graph retriver module * Change type annotations, change return format * Add graph retriever that executes questions as sparql queries * Linking only those entities that are in the knowledge graph * Added logging and using relations extracted from Knowledge graph for linking * Preventing entity linking from linking the same token to multiple entities * Pruning triples that have no variables for select and count queries * Support knowledge graphs with Pipelines * Add text2sparql * Entity linking and relation linking consider more special cases now based on evaluation on labelled data * Separating example code from KGQA implementation * Add eval on combined extarctive and kg questions * Remove references to hp-test * Add fields sparql_query and long_answer_list to metadata * Removing modular Question2SPARQL approach * Removing additional classes used for modular kgqa approach * preparing lcquad data * change graph db * Translating namespaces in knowledge graph queries * Creating graphdb index and loading triples from .ttl file * Fetching graph config files, triples and model from S3 * Fix incompatibility issues with BaseGraphRetriever and BaseComponent * Removing unused utility functions * Adding doc strings and tutorial header * Adding sparqlwrapper dependency * Moving tutorial header * Sorting tutorials by number within name of notebook * Add latest docstring and tutorial changes * Creating test cases for knowledge graph * Changing knowledge graph example to harry potter * Add latest docstring and tutorial changes * Adapting the tutorial notebook to harry potter example * Add GraphDB fixture for tests * Add latest docstring and tutorial changes * Added GraphDB docker launch to CI * Use correct GraphDB fixture * Check if GraphDB instance is already running * Renaming question/query and incorporating other feedback from Timo and Tanay * Removed type annotation * Add latest docstring and tutorial changes Co-authored-by: oryx1729 <oryx1729@protonmail.com> Co-authored-by: Timo Moeller <timo.moeller@deepset.ai> Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>
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assert result[0][0] == "https://deepset.ai/harry_potter/Otter"