rename some variables

app.py

@@ -1,14 +1,14 @@
 import gradio as gr
 import pandas as pd
 
-from query import default_probe, get_scores
+from query import default_probe, get_retrieval_span_scores
 
 
 def spaces_probe(question: str):
     answers, scores, context = default_probe(question)
 
     answers_text = [answer.text for answer in answers]
-    d_scores, s_scores = get_scores(answers, scores, context)
+    d_scores, s_scores = get_retrieval_span_scores(answers)
 
     formatted_result = pd.DataFrame(zip(answers_text, d_scores.tolist(), s_scores.tolist()), columns=[
         "answer", "document score", "span score"])

main.py

@@ -22,19 +22,15 @@ transformers.logging.set_verbosity_error()
 
 if __name__ == '__main__':
     dataset_name = "GroNLP/ik-nlp-22_slp"
-    paragraphs = load_dataset(dataset_name, "paragraphs")
+    paragraphs = cast(DatasetDict, load_dataset(
+        "GroNLP/ik-nlp-22_slp", "paragraphs"))
     questions = cast(DatasetDict, load_dataset(dataset_name, "questions"))
 
     questions_test = questions["test"]
 
-    # logger.info(questions)
-
-    dataset_paragraphs = cast(DatasetDict, load_dataset(
-        "GroNLP/ik-nlp-22_slp", "paragraphs"))
-
     # Initialize retriever
-    retriever = FaissRetriever(dataset_paragraphs)
-    #retriever = ESRetriever(dataset_paragraphs)
+    retriever = FaissRetriever(paragraphs)
+    #retriever = ESRetriever(paragraphs)
 
     # Retrieve example
     # random.seed(111)
@@ -45,6 +41,7 @@ if __name__ == '__main__':
     scores, result = retriever.retrieve(example_q)
     reader_input = context_to_reader_input(result)
 
+    # TODO: use new code from query.py to clean this up
     # Initialize reader
     reader = DprReader()
     answers = reader.read(example_q, reader_input)

poetry.lock

@@ -64,6 +64,14 @@ doc = ["packaging", "sphinx-rtd-theme", "sphinx-autodoc-typehints (>=1.2.0)"]
 test = ["coverage[toml] (>=4.5)", "hypothesis (>=4.0)", "pytest (>=6.0)", "pytest-mock (>=3.6.1)", "trustme", "contextlib2", "uvloop (<0.15)", "mock (>=4)", "uvloop (>=0.15)"]
 trio = ["trio (>=0.16)"]
 
+[[package]]
+name = "appnope"
+version = "0.1.2"
+description = "Disable App Nap on macOS >= 10.9"
+category = "dev"
+optional = false
+python-versions = "*"
+
 [[package]]
 name = "asgiref"
 version = "3.5.0"
@@ -75,6 +83,20 @@ python-versions = ">=3.7"
 [package.extras]
 tests = ["pytest", "pytest-asyncio", "mypy (>=0.800)"]
 
+[[package]]
+name = "asttokens"
+version = "2.0.5"
+description = "Annotate AST trees with source code positions"
+category = "dev"
+optional = false
+python-versions = "*"
+
+[package.dependencies]
+six = "*"
+
+[package.extras]
+test = ["astroid", "pytest"]
+
 [[package]]
 name = "async-timeout"
 version = "4.0.2"
@@ -109,6 +131,14 @@ python-versions = "*"
 pycodestyle = ">=2.8.0"
 toml = "*"
 
+[[package]]
+name = "backcall"
+version = "0.2.0"
+description = "Specifications for callback functions passed in to an API"
+category = "dev"
+optional = false
+python-versions = "*"
+
 [[package]]
 name = "backoff"
 version = "1.10.0"
@@ -236,16 +266,32 @@ xxhash = "*"
 apache-beam = ["apache-beam (>=2.26.0)"]
 audio = ["librosa"]
 benchmarks = ["numpy (==1.18.5)", "tensorflow (==2.3.0)", "torch (==1.6.0)", "transformers (==3.0.2)"]
-dev = ["absl-py", "pytest", "pytest-datadir", "pytest-xdist", "apache-beam (>=2.26.0)", "elasticsearch (<8.0.0)", "aiobotocore", "boto3", "botocore", "faiss-cpu (>=1.6.4)", "fsspec", "moto[server,s3] (==2.0.4)", "rarfile (>=4.0)", "s3fs (==2021.08.1)", "tensorflow (>=2.3,!=2.6.0,!=2.6.1)", "torch", "torchaudio", "soundfile", "transformers", "bs4", "conllu", "h5py", "langdetect", "lxml", "mwparserfromhell", "nltk", "openpyxl", "py7zr", "tldextract", "zstandard", "bert-score (>=0.3.6)", "rouge-score", "sacrebleu", "scipy", "seqeval", "scikit-learn", "jiwer", "sentencepiece", "torchmetrics (==0.6.0)", "mauve-text", "toml (>=0.10.1)", "requests-file (>=1.5.1)", "tldextract (>=3.1.0)", "texttable (>=1.6.3)", "Werkzeug (>=1.0.1)", "six (>=1.15.0,<1.16.0)", "Pillow (>=6.2.1)", "librosa", "wget (>=3.2)", "pytorch-nlp (==0.5.0)", "pytorch-lightning", "fastBPE (==0.1.0)", "fairseq", "black (>=22.0,<23.0)", "flake8 (>=3.8.3)", "isort (>=5.0.0)", "pyyaml (>=5.3.1)", "importlib-resources"]
+dev = ["absl-py", "pytest", "pytest-datadir", "pytest-xdist", "apache-beam (>=2.26.0)", "elasticsearch (<8.0.0)", "aiobotocore", "boto3", "botocore", "faiss-cpu (>=1.6.4)", "fsspec", "moto[s3,server] (==2.0.4)", "rarfile (>=4.0)", "s3fs (==2021.08.1)", "tensorflow (>=2.3,!=2.6.0,!=2.6.1)", "torch", "torchaudio", "soundfile", "transformers", "bs4", "conllu", "h5py", "langdetect", "lxml", "mwparserfromhell", "nltk", "openpyxl", "py7zr", "tldextract", "zstandard", "bert-score (>=0.3.6)", "rouge-score", "sacrebleu", "scipy", "seqeval", "scikit-learn", "jiwer", "sentencepiece", "torchmetrics (==0.6.0)", "mauve-text", "toml (>=0.10.1)", "requests-file (>=1.5.1)", "tldextract (>=3.1.0)", "texttable (>=1.6.3)", "Werkzeug (>=1.0.1)", "six (>=1.15.0,<1.16.0)", "Pillow (>=6.2.1)", "librosa", "wget (>=3.2)", "pytorch-nlp (==0.5.0)", "pytorch-lightning", "fastBPE (==0.1.0)", "fairseq", "black (>=22.0,<23.0)", "flake8 (>=3.8.3)", "isort (>=5.0.0)", "pyyaml (>=5.3.1)", "importlib-resources"]
 docs = ["docutils (==0.16.0)", "recommonmark", "sphinx (==3.1.2)", "sphinx-markdown-tables", "sphinx-rtd-theme (==0.4.3)", "sphinxext-opengraph (==0.4.1)", "sphinx-copybutton", "fsspec (<2021.9.0)", "s3fs", "sphinx-panels", "sphinx-inline-tabs", "myst-parser", "Markdown (!=3.3.5)"]
 quality = ["black (>=22.0,<23.0)", "flake8 (>=3.8.3)", "isort (>=5.0.0)", "pyyaml (>=5.3.1)"]
 s3 = ["fsspec", "boto3", "botocore", "s3fs"]
 tensorflow = ["tensorflow (>=2.2.0,!=2.6.0,!=2.6.1)"]
 tensorflow_gpu = ["tensorflow-gpu (>=2.2.0,!=2.6.0,!=2.6.1)"]
-tests = ["absl-py", "pytest", "pytest-datadir", "pytest-xdist", "apache-beam (>=2.26.0)", "elasticsearch (<8.0.0)", "aiobotocore", "boto3", "botocore", "faiss-cpu (>=1.6.4)", "fsspec", "moto[server,s3] (==2.0.4)", "rarfile (>=4.0)", "s3fs (==2021.08.1)", "tensorflow (>=2.3,!=2.6.0,!=2.6.1)", "torch", "torchaudio", "soundfile", "transformers", "bs4", "conllu", "h5py", "langdetect", "lxml", "mwparserfromhell", "nltk", "openpyxl", "py7zr", "tldextract", "zstandard", "bert-score (>=0.3.6)", "rouge-score", "sacrebleu", "scipy", "seqeval", "scikit-learn", "jiwer", "sentencepiece", "torchmetrics (==0.6.0)", "mauve-text", "toml (>=0.10.1)", "requests-file (>=1.5.1)", "tldextract (>=3.1.0)", "texttable (>=1.6.3)", "Werkzeug (>=1.0.1)", "six (>=1.15.0,<1.16.0)", "Pillow (>=6.2.1)", "librosa", "wget (>=3.2)", "pytorch-nlp (==0.5.0)", "pytorch-lightning", "fastBPE (==0.1.0)", "fairseq", "importlib-resources"]
+tests = ["absl-py", "pytest", "pytest-datadir", "pytest-xdist", "apache-beam (>=2.26.0)", "elasticsearch (<8.0.0)", "aiobotocore", "boto3", "botocore", "faiss-cpu (>=1.6.4)", "fsspec", "moto[s3,server] (==2.0.4)", "rarfile (>=4.0)", "s3fs (==2021.08.1)", "tensorflow (>=2.3,!=2.6.0,!=2.6.1)", "torch", "torchaudio", "soundfile", "transformers", "bs4", "conllu", "h5py", "langdetect", "lxml", "mwparserfromhell", "nltk", "openpyxl", "py7zr", "tldextract", "zstandard", "bert-score (>=0.3.6)", "rouge-score", "sacrebleu", "scipy", "seqeval", "scikit-learn", "jiwer", "sentencepiece", "torchmetrics (==0.6.0)", "mauve-text", "toml (>=0.10.1)", "requests-file (>=1.5.1)", "tldextract (>=3.1.0)", "texttable (>=1.6.3)", "Werkzeug (>=1.0.1)", "six (>=1.15.0,<1.16.0)", "Pillow (>=6.2.1)", "librosa", "wget (>=3.2)", "pytorch-nlp (==0.5.0)", "pytorch-lightning", "fastBPE (==0.1.0)", "fairseq", "importlib-resources"]
 torch = ["torch"]
 vision = ["Pillow (>=6.2.1)"]
 
+[[package]]
+name = "debugpy"
+version = "1.6.0"
+description = "An implementation of the Debug Adapter Protocol for Python"
+category = "dev"
+optional = false
+python-versions = ">=3.7"
+
+[[package]]
+name = "decorator"
+version = "5.1.1"
+description = "Decorators for Humans"
+category = "dev"
+optional = false
+python-versions = ">=3.5"
+
 [[package]]
 name = "dill"
 version = "0.3.4"
@@ -287,6 +333,22 @@ elastic-transport = ">=8,<9"
 async = ["aiohttp (>=3,<4)"]
 requests = ["requests (>=2.4.0,<3.0.0)"]
 
+[[package]]
+name = "entrypoints"
+version = "0.4"
+description = "Discover and load entry points from installed packages."
+category = "dev"
+optional = false
+python-versions = ">=3.6"
+
+[[package]]
+name = "executing"
+version = "0.8.3"
+description = "Get the currently executing AST node of a frame, and other information"
+category = "dev"
+optional = false
+python-versions = "*"
+
 [[package]]
 name = "faiss-cpu"
 version = "1.7.2"
@@ -475,6 +537,78 @@ category = "main"
 optional = false
 python-versions = ">=3.5"
 
+[[package]]
+name = "ipykernel"
+version = "6.11.0"
+description = "IPython Kernel for Jupyter"
+category = "dev"
+optional = false
+python-versions = ">=3.7"
+
+[package.dependencies]
+appnope = {version = "*", markers = "platform_system == \"Darwin\""}
+debugpy = ">=1.0"
+ipython = ">=7.23.1"
+jupyter-client = ">=6.1.12"
+matplotlib-inline = ">=0.1"
+nest-asyncio = "*"
+psutil = "*"
+tornado = ">=6.1"
+traitlets = ">=5.1.0"
+
+[package.extras]
+test = ["pytest (>=6.0)", "pytest-cov", "flaky", "ipyparallel", "pre-commit", "pytest-timeout"]
+
+[[package]]
+name = "ipython"
+version = "8.2.0"
+description = "IPython: Productive Interactive Computing"
+category = "dev"
+optional = false
+python-versions = ">=3.8"
+
+[package.dependencies]
+appnope = {version = "*", markers = "sys_platform == \"darwin\""}
+backcall = "*"
+colorama = {version = "*", markers = "sys_platform == \"win32\""}
+decorator = "*"
+jedi = ">=0.16"
+matplotlib-inline = "*"
+pexpect = {version = ">4.3", markers = "sys_platform != \"win32\""}
+pickleshare = "*"
+prompt-toolkit = ">=2.0.0,<3.0.0 || >3.0.0,<3.0.1 || >3.0.1,<3.1.0"
+pygments = ">=2.4.0"
+stack-data = "*"
+traitlets = ">=5"
+
+[package.extras]
+all = ["black", "Sphinx (>=1.3)", "ipykernel", "nbconvert", "nbformat", "ipywidgets", "notebook", "ipyparallel", "qtconsole", "pytest (<7.1)", "pytest-asyncio", "testpath", "curio", "matplotlib (!=3.2.0)", "numpy (>=1.19)", "pandas", "trio"]
+black = ["black"]
+doc = ["Sphinx (>=1.3)"]
+kernel = ["ipykernel"]
+nbconvert = ["nbconvert"]
+nbformat = ["nbformat"]
+notebook = ["ipywidgets", "notebook"]
+parallel = ["ipyparallel"]
+qtconsole = ["qtconsole"]
+test = ["pytest (<7.1)", "pytest-asyncio", "testpath"]
+test_extra = ["pytest (<7.1)", "pytest-asyncio", "testpath", "curio", "matplotlib (!=3.2.0)", "nbformat", "numpy (>=1.19)", "pandas", "trio"]
+
+[[package]]
+name = "jedi"
+version = "0.18.1"
+description = "An autocompletion tool for Python that can be used for text editors."
+category = "dev"
+optional = false
+python-versions = ">=3.6"
+
+[package.dependencies]
+parso = ">=0.8.0,<0.9.0"
+
+[package.extras]
+qa = ["flake8 (==3.8.3)", "mypy (==0.782)"]
+testing = ["Django (<3.1)", "colorama", "docopt", "pytest (<7.0.0)"]
+
 [[package]]
 name = "jinja2"
 version = "3.1.1"
@@ -497,6 +631,39 @@ category = "main"
 optional = false
 python-versions = ">=3.6"
 
+[[package]]
+name = "jupyter-client"
+version = "7.2.1"
+description = "Jupyter protocol implementation and client libraries"
+category = "dev"
+optional = false
+python-versions = ">=3.7"
+
+[package.dependencies]
+entrypoints = "*"
+jupyter-core = ">=4.9.2"
+nest-asyncio = ">=1.5.4"
+python-dateutil = ">=2.8.2"
+pyzmq = ">=22.3"
+tornado = ">=6.0"
+traitlets = "*"
+
+[package.extras]
+doc = ["ipykernel", "myst-parser", "sphinx (>=1.3.6)", "sphinx-rtd-theme", "sphinxcontrib-github-alt"]
+test = ["codecov", "coverage", "ipykernel (>=6.5)", "ipython", "mypy", "pre-commit", "pytest", "pytest-asyncio (>=0.18)", "pytest-cov", "pytest-timeout"]
+
+[[package]]
+name = "jupyter-core"
+version = "4.9.2"
+description = "Jupyter core package. A base package on which Jupyter projects rely."
+category = "dev"
+optional = false
+python-versions = ">=3.6"
+
+[package.dependencies]
+pywin32 = {version = ">=1.0", markers = "sys_platform == \"win32\" and platform_python_implementation != \"PyPy\""}
+traitlets = "*"
+
 [[package]]
 name = "kiwisolver"
 version = "1.4.2"
@@ -572,6 +739,17 @@ pyparsing = ">=2.2.1"
 python-dateutil = ">=2.7"
 setuptools_scm = ">=4"
 
+[[package]]
+name = "matplotlib-inline"
+version = "0.1.3"
+description = "Inline Matplotlib backend for Jupyter"
+category = "dev"
+optional = false
+python-versions = ">=3.5"
+
+[package.dependencies]
+traitlets = "*"
+
 [[package]]
 name = "mccabe"
 version = "0.6.1"
@@ -657,6 +835,14 @@ category = "dev"
 optional = false
 python-versions = "*"
 
+[[package]]
+name = "nest-asyncio"
+version = "1.5.4"
+description = "Patch asyncio to allow nested event loops"
+category = "dev"
+optional = false
+python-versions = ">=3.5"
+
 [[package]]
 name = "numpy"
 version = "1.22.3"
@@ -725,6 +911,37 @@ ed25519 = ["pynacl (>=1.0.1)", "bcrypt (>=3.1.3)"]
 gssapi = ["pyasn1 (>=0.1.7)", "gssapi (>=1.4.1)", "pywin32 (>=2.1.8)"]
 invoke = ["invoke (>=1.3)"]
 
+[[package]]
+name = "parso"
+version = "0.8.3"
+description = "A Python Parser"
+category = "dev"
+optional = false
+python-versions = ">=3.6"
+
+[package.extras]
+qa = ["flake8 (==3.8.3)", "mypy (==0.782)"]
+testing = ["docopt", "pytest (<6.0.0)"]
+
+[[package]]
+name = "pexpect"
+version = "4.8.0"
+description = "Pexpect allows easy control of interactive console applications."
+category = "dev"
+optional = false
+python-versions = "*"
+
+[package.dependencies]
+ptyprocess = ">=0.5"
+
+[[package]]
+name = "pickleshare"
+version = "0.7.5"
+description = "Tiny 'shelve'-like database with concurrency support"
+category = "dev"
+optional = false
+python-versions = "*"
+
 [[package]]
 name = "pillow"
 version = "9.0.1"
@@ -733,6 +950,55 @@ category = "main"
 optional = false
 python-versions = ">=3.7"
 
+[[package]]
+name = "prompt-toolkit"
+version = "3.0.28"
+description = "Library for building powerful interactive command lines in Python"
+category = "dev"
+optional = false
+python-versions = ">=3.6.2"
+
+[package.dependencies]
+wcwidth = "*"
+
+[[package]]
+name = "psutil"
+version = "5.9.0"
+description = "Cross-platform lib for process and system monitoring in Python."
+category = "dev"
+optional = false
+python-versions = ">=2.6, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*"
+
+[package.extras]
+test = ["ipaddress", "mock", "unittest2", "enum34", "pywin32", "wmi"]
+
+[[package]]
+name = "ptyprocess"
+version = "0.7.0"
+description = "Run a subprocess in a pseudo terminal"
+category = "dev"
+optional = false
+python-versions = "*"
+
+[[package]]
+name = "pure-eval"
+version = "0.2.2"
+description = "Safely evaluate AST nodes without side effects"
+category = "dev"
+optional = false
+python-versions = "*"
+
+[package.extras]
+tests = ["pytest"]
+
+[[package]]
+name = "py"
+version = "1.11.0"
+description = "library with cross-python path, ini-parsing, io, code, log facilities"
+category = "dev"
+optional = false
+python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*"
+
 [[package]]
 name = "pyarrow"
 version = "7.0.0"
@@ -799,6 +1065,14 @@ category = "dev"
 optional = false
 python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*"
 
+[[package]]
+name = "pygments"
+version = "2.11.2"
+description = "Pygments is a syntax highlighting package written in Python."
+category = "dev"
+optional = false
+python-versions = ">=3.5"
+
 [[package]]
 name = "pynacl"
 version = "1.5.0"
@@ -866,6 +1140,14 @@ category = "main"
 optional = false
 python-versions = "*"
 
+[[package]]
+name = "pywin32"
+version = "303"
+description = "Python for Window Extensions"
+category = "dev"
+optional = false
+python-versions = "*"
+
 [[package]]
 name = "pyyaml"
 version = "6.0"
@@ -874,6 +1156,18 @@ category = "main"
 optional = false
 python-versions = ">=3.6"
 
+[[package]]
+name = "pyzmq"
+version = "22.3.0"
+description = "Python bindings for 0MQ"
+category = "dev"
+optional = false
+python-versions = ">=3.6"
+
+[package.dependencies]
+cffi = {version = "*", markers = "implementation_name == \"pypy\""}
+py = {version = "*", markers = "implementation_name == \"pypy\""}
+
 [[package]]
 name = "regex"
 version = "2022.3.2"
@@ -962,6 +1256,22 @@ category = "main"
 optional = false
 python-versions = ">=3.5"
 
+[[package]]
+name = "stack-data"
+version = "0.2.0"
+description = "Extract data from python stack frames and tracebacks for informative displays"
+category = "dev"
+optional = false
+python-versions = "*"
+
+[package.dependencies]
+asttokens = "*"
+executing = "*"
+pure-eval = "*"
+
+[package.extras]
+tests = ["pytest", "typeguard", "pygments", "littleutils", "cython"]
+
 [[package]]
 name = "starlette"
 version = "0.17.1"
@@ -1015,6 +1325,14 @@ python-versions = ">=3.7.0"
 [package.dependencies]
 typing-extensions = "*"
 
+[[package]]
+name = "tornado"
+version = "6.1"
+description = "Tornado is a Python web framework and asynchronous networking library, originally developed at FriendFeed."
+category = "dev"
+optional = false
+python-versions = ">= 3.5"
+
 [[package]]
 name = "tqdm"
 version = "4.63.0"
@@ -1031,6 +1349,17 @@ dev = ["py-make (>=0.1.0)", "twine", "wheel"]
 notebook = ["ipywidgets (>=6)"]
 telegram = ["requests"]
 
+[[package]]
+name = "traitlets"
+version = "5.1.1"
+description = "Traitlets Python configuration system"
+category = "dev"
+optional = false
+python-versions = ">=3.7"
+
+[package.extras]
+test = ["pytest"]
+
 [[package]]
 name = "transformers"
 version = "4.17.0"
@@ -1138,6 +1467,14 @@ h11 = ">=0.8"
 [package.extras]
 standard = ["websockets (>=10.0)", "httptools (>=0.4.0)", "watchgod (>=0.6)", "python-dotenv (>=0.13)", "PyYAML (>=5.1)", "uvloop (>=0.14.0,!=0.15.0,!=0.15.1)", "colorama (>=0.4)"]
 
+[[package]]
+name = "wcwidth"
+version = "0.2.5"
+description = "Measures the displayed width of unicode strings in a terminal"
+category = "dev"
+optional = false
+python-versions = "*"
+
 [[package]]
 name = "xxhash"
 version = "3.0.0"
@@ -1161,7 +1498,7 @@ multidict = ">=4.0"
 [metadata]
 lock-version = "1.1"
 python-versions = "^3.8"
-content-hash = "f9cd67e84579566c7d72a536f9330ec56818e74e923f1772eb4f1621c4f9407f"
+content-hash = "a9ce48f30c8568321f3f4576e1c4987ef94a4216201ba4bce2dc719c397d5da6"
 
 [metadata.files]
 aiohttp = [
@@ -1250,10 +1587,18 @@ anyio = [
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+    {file = "pyzmq-22.3.0-cp39-cp39-musllinux_1_1_i686.whl", hash = "sha256:53f4fd13976789ffafedd4d46f954c7bb01146121812b72b4ddca286034df966"},
+    {file = "pyzmq-22.3.0-cp39-cp39-musllinux_1_1_x86_64.whl", hash = "sha256:d1b5d457acbadcf8b27561deeaa386b0217f47626b29672fa7bd31deb6e91e1b"},
+    {file = "pyzmq-22.3.0-cp39-cp39-win32.whl", hash = "sha256:e6a02cf7271ee94674a44f4e62aa061d2d049001c844657740e156596298b70b"},
+    {file = "pyzmq-22.3.0-cp39-cp39-win_amd64.whl", hash = "sha256:d3dcb5548ead4f1123851a5ced467791f6986d68c656bc63bfff1bf9e36671e2"},
+    {file = "pyzmq-22.3.0-pp37-pypy37_pp73-macosx_10_9_x86_64.whl", hash = "sha256:3a4c9886d61d386b2b493377d980f502186cd71d501fffdba52bd2a0880cef4f"},
+    {file = "pyzmq-22.3.0-pp37-pypy37_pp73-manylinux_2_12_i686.manylinux2010_i686.whl", hash = "sha256:80e043a89c6cadefd3a0712f8a1322038e819ebe9dbac7eca3bce1721bcb63bf"},
+    {file = "pyzmq-22.3.0-pp37-pypy37_pp73-manylinux_2_12_x86_64.manylinux2010_x86_64.whl", hash = "sha256:1621e7a2af72cced1f6ec8ca8ca91d0f76ac236ab2e8828ac8fe909512d566cb"},
+    {file = "pyzmq-22.3.0-pp37-pypy37_pp73-win_amd64.whl", hash = "sha256:d6157793719de168b199194f6b6173f0ccd3bf3499e6870fac17086072e39115"},
+    {file = "pyzmq-22.3.0.tar.gz", hash = "sha256:8eddc033e716f8c91c6a2112f0a8ebc5e00532b4a6ae1eb0ccc48e027f9c671c"},
+]
 regex = [
     {file = "regex-2022.3.2-cp310-cp310-macosx_10_9_x86_64.whl", hash = "sha256:ab69b4fe09e296261377d209068d52402fb85ef89dc78a9ac4a29a895f4e24a7"},
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@@ -2184,6 +2722,10 @@ sniffio = [
     {file = "sniffio-1.2.0-py3-none-any.whl", hash = "sha256:471b71698eac1c2112a40ce2752bb2f4a4814c22a54a3eed3676bc0f5ca9f663"},
     {file = "sniffio-1.2.0.tar.gz", hash = "sha256:c4666eecec1d3f50960c6bdf61ab7bc350648da6c126e3cf6898d8cd4ddcd3de"},
 ]
+stack-data = [
+    {file = "stack_data-0.2.0-py3-none-any.whl", hash = "sha256:999762f9c3132308789affa03e9271bbbe947bf78311851f4d485d8402ed858e"},
+    {file = "stack_data-0.2.0.tar.gz", hash = "sha256:45692d41bd633a9503a5195552df22b583caf16f0b27c4e58c98d88c8b648e12"},
+]
 starlette = [
     {file = "starlette-0.17.1-py3-none-any.whl", hash = "sha256:26a18cbda5e6b651c964c12c88b36d9898481cd428ed6e063f5f29c418f73050"},
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@@ -2257,10 +2799,57 @@ torch = [
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     {file = "torch-1.11.0-cp39-none-macosx_11_0_arm64.whl", hash = "sha256:0e48af66ad755f0f9c5f2664028a414f57c49d6adc37e77e06fe0004da4edb61"},
 ]
+tornado = [
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+    {file = "tornado-6.1-cp35-cp35m-manylinux1_i686.whl", hash = "sha256:0d321a39c36e5f2c4ff12b4ed58d41390460f798422c4504e09eb5678e09998c"},
+    {file = "tornado-6.1-cp35-cp35m-manylinux1_x86_64.whl", hash = "sha256:9de9e5188a782be6b1ce866e8a51bc76a0fbaa0e16613823fc38e4fc2556ad05"},
+    {file = "tornado-6.1-cp35-cp35m-manylinux2010_i686.whl", hash = "sha256:61b32d06ae8a036a6607805e6720ef00a3c98207038444ba7fd3d169cd998910"},
+    {file = "tornado-6.1-cp35-cp35m-manylinux2010_x86_64.whl", hash = "sha256:3e63498f680547ed24d2c71e6497f24bca791aca2fe116dbc2bd0ac7f191691b"},
+    {file = "tornado-6.1-cp35-cp35m-manylinux2014_aarch64.whl", hash = "sha256:6c77c9937962577a6a76917845d06af6ab9197702a42e1346d8ae2e76b5e3675"},
+    {file = "tornado-6.1-cp35-cp35m-win32.whl", hash = "sha256:6286efab1ed6e74b7028327365cf7346b1d777d63ab30e21a0f4d5b275fc17d5"},
+    {file = "tornado-6.1-cp35-cp35m-win_amd64.whl", hash = "sha256:fa2ba70284fa42c2a5ecb35e322e68823288a4251f9ba9cc77be04ae15eada68"},
+    {file = "tornado-6.1-cp36-cp36m-macosx_10_9_x86_64.whl", hash = "sha256:0a00ff4561e2929a2c37ce706cb8233b7907e0cdc22eab98888aca5dd3775feb"},
+    {file = "tornado-6.1-cp36-cp36m-manylinux1_i686.whl", hash = "sha256:748290bf9112b581c525e6e6d3820621ff020ed95af6f17fedef416b27ed564c"},
+    {file = "tornado-6.1-cp36-cp36m-manylinux1_x86_64.whl", hash = "sha256:e385b637ac3acaae8022e7e47dfa7b83d3620e432e3ecb9a3f7f58f150e50921"},
+    {file = "tornado-6.1-cp36-cp36m-manylinux2010_i686.whl", hash = "sha256:25ad220258349a12ae87ede08a7b04aca51237721f63b1808d39bdb4b2164558"},
+    {file = "tornado-6.1-cp36-cp36m-manylinux2010_x86_64.whl", hash = "sha256:65d98939f1a2e74b58839f8c4dab3b6b3c1ce84972ae712be02845e65391ac7c"},
+    {file = "tornado-6.1-cp36-cp36m-manylinux2014_aarch64.whl", hash = "sha256:e519d64089b0876c7b467274468709dadf11e41d65f63bba207e04217f47c085"},
+    {file = "tornado-6.1-cp36-cp36m-win32.whl", hash = "sha256:b87936fd2c317b6ee08a5741ea06b9d11a6074ef4cc42e031bc6403f82a32575"},
+    {file = "tornado-6.1-cp36-cp36m-win_amd64.whl", hash = "sha256:cc0ee35043162abbf717b7df924597ade8e5395e7b66d18270116f8745ceb795"},
+    {file = "tornado-6.1-cp37-cp37m-macosx_10_9_x86_64.whl", hash = "sha256:7250a3fa399f08ec9cb3f7b1b987955d17e044f1ade821b32e5f435130250d7f"},
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+    {file = "tornado-6.1-cp37-cp37m-manylinux1_x86_64.whl", hash = "sha256:dcef026f608f678c118779cd6591c8af6e9b4155c44e0d1bc0c87c036fb8c8c4"},
+    {file = "tornado-6.1-cp37-cp37m-manylinux2010_i686.whl", hash = "sha256:70dec29e8ac485dbf57481baee40781c63e381bebea080991893cd297742b8fd"},
+    {file = "tornado-6.1-cp37-cp37m-manylinux2010_x86_64.whl", hash = "sha256:d3f7594930c423fd9f5d1a76bee85a2c36fd8b4b16921cae7e965f22575e9c01"},
+    {file = "tornado-6.1-cp37-cp37m-manylinux2014_aarch64.whl", hash = "sha256:3447475585bae2e77ecb832fc0300c3695516a47d46cefa0528181a34c5b9d3d"},
+    {file = "tornado-6.1-cp37-cp37m-win32.whl", hash = "sha256:e7229e60ac41a1202444497ddde70a48d33909e484f96eb0da9baf8dc68541df"},
+    {file = "tornado-6.1-cp37-cp37m-win_amd64.whl", hash = "sha256:cb5ec8eead331e3bb4ce8066cf06d2dfef1bfb1b2a73082dfe8a161301b76e37"},
+    {file = "tornado-6.1-cp38-cp38-macosx_10_9_x86_64.whl", hash = "sha256:20241b3cb4f425e971cb0a8e4ffc9b0a861530ae3c52f2b0434e6c1b57e9fd95"},
+    {file = "tornado-6.1-cp38-cp38-manylinux1_i686.whl", hash = "sha256:c77da1263aa361938476f04c4b6c8916001b90b2c2fdd92d8d535e1af48fba5a"},
+    {file = "tornado-6.1-cp38-cp38-manylinux1_x86_64.whl", hash = "sha256:fba85b6cd9c39be262fcd23865652920832b61583de2a2ca907dbd8e8a8c81e5"},
+    {file = "tornado-6.1-cp38-cp38-manylinux2010_i686.whl", hash = "sha256:1e8225a1070cd8eec59a996c43229fe8f95689cb16e552d130b9793cb570a288"},
+    {file = "tornado-6.1-cp38-cp38-manylinux2010_x86_64.whl", hash = "sha256:d14d30e7f46a0476efb0deb5b61343b1526f73ebb5ed84f23dc794bdb88f9d9f"},
+    {file = "tornado-6.1-cp38-cp38-manylinux2014_aarch64.whl", hash = "sha256:8f959b26f2634a091bb42241c3ed8d3cedb506e7c27b8dd5c7b9f745318ddbb6"},
+    {file = "tornado-6.1-cp38-cp38-win32.whl", hash = "sha256:34ca2dac9e4d7afb0bed4677512e36a52f09caa6fded70b4e3e1c89dbd92c326"},
+    {file = "tornado-6.1-cp38-cp38-win_amd64.whl", hash = "sha256:6196a5c39286cc37c024cd78834fb9345e464525d8991c21e908cc046d1cc02c"},
+    {file = "tornado-6.1-cp39-cp39-macosx_10_9_x86_64.whl", hash = "sha256:f0ba29bafd8e7e22920567ce0d232c26d4d47c8b5cf4ed7b562b5db39fa199c5"},
+    {file = "tornado-6.1-cp39-cp39-manylinux1_i686.whl", hash = "sha256:33892118b165401f291070100d6d09359ca74addda679b60390b09f8ef325ffe"},
+    {file = "tornado-6.1-cp39-cp39-manylinux1_x86_64.whl", hash = "sha256:7da13da6f985aab7f6f28debab00c67ff9cbacd588e8477034c0652ac141feea"},
+    {file = "tornado-6.1-cp39-cp39-manylinux2010_i686.whl", hash = "sha256:e0791ac58d91ac58f694d8d2957884df8e4e2f6687cdf367ef7eb7497f79eaa2"},
+    {file = "tornado-6.1-cp39-cp39-manylinux2010_x86_64.whl", hash = "sha256:66324e4e1beede9ac79e60f88de548da58b1f8ab4b2f1354d8375774f997e6c0"},
+    {file = "tornado-6.1-cp39-cp39-manylinux2014_aarch64.whl", hash = "sha256:a48900ecea1cbb71b8c71c620dee15b62f85f7c14189bdeee54966fbd9a0c5bd"},
+    {file = "tornado-6.1-cp39-cp39-win32.whl", hash = "sha256:d3d20ea5782ba63ed13bc2b8c291a053c8d807a8fa927d941bd718468f7b950c"},
+    {file = "tornado-6.1-cp39-cp39-win_amd64.whl", hash = "sha256:548430be2740e327b3fe0201abe471f314741efcb0067ec4f2d7dcfb4825f3e4"},
+    {file = "tornado-6.1.tar.gz", hash = "sha256:33c6e81d7bd55b468d2e793517c909b139960b6c790a60b7991b9b6b76fb9791"},
+]
 tqdm = [
     {file = "tqdm-4.63.0-py2.py3-none-any.whl", hash = "sha256:e643e071046f17139dea55b880dc9b33822ce21613b4a4f5ea57f202833dbc29"},
     {file = "tqdm-4.63.0.tar.gz", hash = "sha256:1d9835ede8e394bb8c9dcbffbca02d717217113adc679236873eeaac5bc0b3cd"},
 ]
+traitlets = [
+    {file = "traitlets-5.1.1-py3-none-any.whl", hash = "sha256:2d313cc50a42cd6c277e7d7dc8d4d7fedd06a2c215f78766ae7b1a66277e0033"},
+    {file = "traitlets-5.1.1.tar.gz", hash = "sha256:059f456c5a7c1c82b98c2e8c799f39c9b8128f6d0d46941ee118daace9eb70c7"},
+]
 transformers = [
     {file = "transformers-4.17.0-py3-none-any.whl", hash = "sha256:5c7d1955693ebf4a69a0fa700b2ef730232d5d7c1528e15d44c1d473b38f57b8"},
     {file = "transformers-4.17.0.tar.gz", hash = "sha256:986fd59255460555b893a2b1827b9b8dd4e5cd6343e4409d18539208f69fb51b"},
@@ -2281,6 +2870,10 @@ uvicorn = [
     {file = "uvicorn-0.17.6-py3-none-any.whl", hash = "sha256:19e2a0e96c9ac5581c01eb1a79a7d2f72bb479691acd2b8921fce48ed5b961a6"},
     {file = "uvicorn-0.17.6.tar.gz", hash = "sha256:5180f9d059611747d841a4a4c4ab675edf54c8489e97f96d0583ee90ac3bfc23"},
 ]
+wcwidth = [
+    {file = "wcwidth-0.2.5-py2.py3-none-any.whl", hash = "sha256:beb4802a9cebb9144e99086eff703a642a13d6a0052920003a230f3294bbe784"},
+    {file = "wcwidth-0.2.5.tar.gz", hash = "sha256:c4d647b99872929fdb7bdcaa4fbe7f01413ed3d98077df798530e5b04f116c83"},
+]
 xxhash = [
     {file = "xxhash-3.0.0-cp310-cp310-macosx_10_9_x86_64.whl", hash = "sha256:219cba13991fd73cf21a5efdafa5056f0ae0b8f79e5e0112967e3058daf73eea"},
     {file = "xxhash-3.0.0-cp310-cp310-macosx_11_0_arm64.whl", hash = "sha256:3fcbb846af15eff100c412ae54f4974ff277c92eacd41f1ec7803a64fd07fa0c"},

pyproject.toml

@@ -20,6 +20,7 @@ Jinja2 = "^3.1.1"
 flake8 = "^4.0.1"
 autopep8 = "^1.6.0"
 mypy = "^0.941"
+ipykernel = "^6.11.0"
 
 [tool.mypy]
 no_implicit_optional=true

query.py

@@ -2,7 +2,7 @@ import argparse
 import torch
 import transformers
 
-from typing import List, cast
+from typing import List, Literal, Union, cast
 from datasets import load_dataset, DatasetDict
 from dotenv import load_dotenv
 
@@ -14,9 +14,9 @@ from src.utils.preprocessing import context_to_reader_input
 from src.utils.log import get_logger
 
 
-def get_retriever(r: str, ds: DatasetDict) -> Retriever:
+def get_retriever(r: Union[Literal["es"], Literal["fais"]], paragraphs: DatasetDict) -> Retriever:
     retriever = ESRetriever if r == "es" else FaissRetriever
-    return retriever(ds)
+    return retriever(paragraphs)
 
 
 def print_name(contexts: dict, section: str, id: int):
@@ -25,7 +25,7 @@ def print_name(contexts: dict, section: str, id: int):
         print(f"      {section}: {name}")
 
 
-def get_scores(answers: List[tuple], scores: List[float], contexts: dict):
+def get_retrieval_span_scores(answers: List[tuple]):
     # calculate answer scores
     sm = torch.nn.Softmax(dim=0)
     d_scores = sm(torch.Tensor(
@@ -37,7 +37,7 @@ def get_scores(answers: List[tuple], scores: List[float], contexts: dict):
 
 
 def print_answers(answers: List[tuple], scores: List[float], contexts: dict):
-    d_scores, s_scores = get_scores(answers, scores, contexts)
+    d_scores, s_scores = get_retrieval_span_scores(answers)
 
     for pos, answer in enumerate(answers):
         print(f"{pos + 1:>4}. {answer.text}")
@@ -61,8 +61,9 @@ def probe(query: str, retriever: Retriever, reader: DprReader, num_answers: int
 
 def default_probe(query: str):
     # default probe is a probe that prints 5 answers with faiss
-    dataset = cast(DatasetDict, load_dataset("GroNLP/ik-nlp-22_slp"))
-    retriever = get_retriever("faiss", dataset)
+    paragraphs = cast(DatasetDict, load_dataset(
+        "GroNLP/ik-nlp-22_slp", "paragraphs"))
+    retriever = get_retriever("faiss", paragraphs)
     reader = DprReader()
 
     return probe(query, retriever, reader)
@@ -70,10 +71,11 @@ def default_probe(query: str):
 
 def main(args: argparse.Namespace):
     # Initialize dataset
-    dataset = cast(DatasetDict, load_dataset("GroNLP/ik-nlp-22_slp"))
+    paragraphs = cast(DatasetDict, load_dataset(
+        "GroNLP/ik-nlp-22_slp", "paragraphs"))
 
     # Retrieve
-    retriever = get_retriever(args.retriever, dataset)
+    retriever = get_retriever(args.retriever, paragraphs)
     reader = DprReader()
     answers, scores, contexts = probe(
         args.query, retriever, reader, args.num_answers)

src/retrievers/es_retriever.py

@@ -1,16 +1,15 @@
-from datasets import DatasetDict, load_dataset
+from datasets import DatasetDict
 from src.utils.log import get_logger
 from src.retrievers.base_retriever import Retriever
 from elasticsearch import Elasticsearch
-from dotenv import load_dotenv
 import os
 
 logger = get_logger()
 
 
 class ESRetriever(Retriever):
-    def __init__(self, dataset: DatasetDict) -> None:
-        self.dataset = dataset["train"]
+    def __init__(self, paragraphs: DatasetDict) -> None:
+        self.paragraphs = paragraphs["train"]
 
         es_host = os.getenv("ELASTIC_HOST", "localhost")
         es_password = os.getenv("ELASTIC_PASSWORD")
@@ -22,15 +21,15 @@ class ESRetriever(Retriever):
             ca_certs="./http_ca.crt")
 
         if self.client.indices.exists(index="paragraphs"):
-            self.dataset.load_elasticsearch_index(
+            self.paragraphs.load_elasticsearch_index(
                 "paragraphs", es_index_name="paragraphs",
                 es_client=self.client)
         else:
             logger.info(f"Creating index 'paragraphs' on {es_host}")
-            self.dataset.add_elasticsearch_index(column="text",
-                                                 index_name="paragraphs",
-                                                 es_index_name="paragraphs",
-                                                 es_client=self.client)
+            self.paragraphs.add_elasticsearch_index(column="text",
+                                                    index_name="paragraphs",
+                                                    es_index_name="paragraphs",
+                                                    es_client=self.client)
 
     def retrieve(self, query: str, k: int = 5):
-        return self.dataset.get_nearest_examples("paragraphs", query, k)
+        return self.paragraphs.get_nearest_examples("paragraphs", query, k)

src/retrievers/faiss_retriever.py

@@ -27,7 +27,7 @@ class FaissRetriever(Retriever):
     based on https://huggingface.co/docs/datasets/faiss_es#faiss.
     """
 
-    def __init__(self, dataset: DatasetDict, embedding_path: str = "./src/models/paragraphs_embedding.faiss") -> None:
+    def __init__(self, paragraphs: DatasetDict, embedding_path: str = "./src/models/paragraphs_embedding.faiss") -> None:
         torch.set_grad_enabled(False)
 
         # Context encoding and tokenization
@@ -46,7 +46,7 @@ class FaissRetriever(Retriever):
             "facebook/dpr-question_encoder-single-nq-base"
         )
 
-        self.dataset = dataset
+        self.paragraphs = paragraphs
         self.embedding_path = embedding_path
 
         self.index = self._init_index()
@@ -55,10 +55,9 @@ class FaissRetriever(Retriever):
             self,
             force_new_embedding: bool = False):
 
-        ds = self.dataset["train"]
+        ds = self.paragraphs["train"]
         ds = ds.map(remove_formulas)
 
-
         if not force_new_embedding and os.path.exists(self.embedding_path):
             ds.load_faiss_index(
                 'embeddings', self.embedding_path)  # type: ignore