From 1293f8e80237e2abc11339b6af71b0d395ca8ba5 Mon Sep 17 00:00:00 2001
From: caufieldjh <j.harry.caufield@gmail.com>
Date: Wed, 31 Jan 2024 14:14:47 -0500
Subject: [PATCH 1/2] Update poetry lock

---
 poetry.lock | 928 +++++++++++++++++++++++++---------------------------
 1 file changed, 453 insertions(+), 475 deletions(-)

diff --git a/poetry.lock b/poetry.lock
index 8de6f7ba3..c99a1166c 100644
--- a/poetry.lock
+++ b/poetry.lock
@@ -22,87 +22,87 @@ test = ["pytest", "pytest-cov"]
 
 [[package]]
 name = "aiohttp"
-version = "3.9.1"
+version = "3.9.3"
 description = "Async http client/server framework (asyncio)"
 optional = false
 python-versions = ">=3.8"
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 ]
 
 [package.dependencies]
@@ -275,13 +275,13 @@ files = [
 
 [[package]]
 name = "argcomplete"
-version = "3.2.1"
+version = "3.2.2"
 description = "Bash tab completion for argparse"
 optional = true
 python-versions = ">=3.8"
 files = [
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 ]
 
 [package.extras]
@@ -520,17 +520,17 @@ files = [
 
 [[package]]
 name = "boto3"
-version = "1.34.22"
+version = "1.34.31"
 description = "The AWS SDK for Python"
 optional = false
 python-versions = ">= 3.8"
 files = [
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 ]
 
 [package.dependencies]
-botocore = ">=1.34.22,<1.35.0"
+botocore = ">=1.34.31,<1.35.0"
 jmespath = ">=0.7.1,<2.0.0"
 s3transfer = ">=0.10.0,<0.11.0"
 
@@ -539,13 +539,13 @@ crt = ["botocore[crt] (>=1.21.0,<2.0a0)"]
 
 [[package]]
 name = "botocore"
-version = "1.34.22"
+version = "1.34.31"
 description = "Low-level, data-driven core of boto 3."
 optional = false
 python-versions = ">= 3.8"
 files = [
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 ]
 
 [package.dependencies]
@@ -1652,13 +1652,13 @@ rfc3987 = "*"
 
 [[package]]
 name = "furo"
-version = "2023.9.10"
+version = "2024.1.29"
 description = "A clean customisable Sphinx documentation theme."
 optional = true
 python-versions = ">=3.8"
 files = [
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 ]
 
 [package.dependencies]
@@ -1969,13 +1969,13 @@ socks = ["socksio (==1.*)"]
 
 [[package]]
 name = "huggingface-hub"
-version = "0.20.2"
+version = "0.20.3"
 description = "Client library to download and publish models, datasets and other repos on the huggingface.co hub"
 optional = true
 python-versions = ">=3.8.0"
 files = [
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 ]
 
 [package.dependencies]
@@ -2521,29 +2521,29 @@ files = [
 
 [[package]]
 name = "jsonschema"
-version = "4.21.0"
+version = "4.21.1"
 description = "An implementation of JSON Schema validation for Python"
 optional = false
 python-versions = ">=3.8"
 files = [
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 ]
 
 [package.dependencies]
 attrs = ">=22.2.0"
-fqdn = {version = "*", optional = true, markers = "extra == \"format\""}
-idna = {version = "*", optional = true, markers = "extra == \"format\""}
-isoduration = {version = "*", optional = true, markers = "extra == \"format\""}
-jsonpointer = {version = ">1.13", optional = true, markers = "extra == \"format\""}
+fqdn = {version = "*", optional = true, markers = "extra == \"format-nongpl\""}
+idna = {version = "*", optional = true, markers = "extra == \"format-nongpl\""}
+isoduration = {version = "*", optional = true, markers = "extra == \"format-nongpl\""}
+jsonpointer = {version = ">1.13", optional = true, markers = "extra == \"format-nongpl\""}
 jsonschema-specifications = ">=2023.03.6"
 referencing = ">=0.28.4"
-rfc3339-validator = {version = "*", optional = true, markers = "extra == \"format\""}
+rfc3339-validator = {version = "*", optional = true, markers = "extra == \"format-nongpl\""}
 rfc3986-validator = {version = ">0.1.0", optional = true, markers = "extra == \"format-nongpl\""}
 rfc3987 = {version = "*", optional = true, markers = "extra == \"format\""}
 rpds-py = ">=0.7.1"
-uri-template = {version = "*", optional = true, markers = "extra == \"format\""}
-webcolors = {version = ">=1.11", optional = true, markers = "extra == \"format\""}
+uri-template = {version = "*", optional = true, markers = "extra == \"format-nongpl\""}
+webcolors = {version = ">=1.11", optional = true, markers = "extra == \"format-nongpl\""}
 
 [package.extras]
 format = ["fqdn", "idna", "isoduration", "jsonpointer (>1.13)", "rfc3339-validator", "rfc3987", "uri-template", "webcolors (>=1.11)"]
@@ -2738,13 +2738,13 @@ test = ["flaky", "ipykernel", "pre-commit", "pytest (>=7.0)", "pytest-console-sc
 
 [[package]]
 name = "jupyter-server-terminals"
-version = "0.5.1"
+version = "0.5.2"
 description = "A Jupyter Server Extension Providing Terminals."
 optional = false
 python-versions = ">=3.8"
 files = [
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 ]
 
 [package.dependencies]
@@ -2757,13 +2757,13 @@ test = ["jupyter-server (>=2.0.0)", "pytest (>=7.0)", "pytest-jupyter[server] (>
 
 [[package]]
 name = "jupyterlab"
-version = "4.0.11"
+version = "4.0.12"
 description = "JupyterLab computational environment"
 optional = false
 python-versions = ">=3.8"
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 ]
 
 [package.dependencies]
@@ -2999,13 +2999,13 @@ regex = ["regex"]
 
 [[package]]
 name = "linkml"
-version = "1.6.8"
+version = "1.6.10"
 description = "Linked Open Data Modeling Language"
 optional = false
 python-versions = ">=3.8.1,<4.0.0"
 files = [
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 ]
 
 [package.dependencies]
@@ -3142,13 +3142,13 @@ test = ["black", "cogapp", "mypy", "numpy", "pytest", "requests-mock", "ruff", "
 
 [[package]]
 name = "llm-gpt4all"
-version = "0.2"
+version = "0.3"
 description = "Plugin for LLM adding support for GPT4ALL models"
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 python-versions = ">=3.9"
 files = [
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 ]
 
 [package.dependencies]
@@ -3296,71 +3296,71 @@ testing = ["coverage", "pytest", "pytest-cov", "pytest-regressions"]
 
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 [[package]]
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 [package.dependencies]
@@ -4162,31 +4166,31 @@ numpy = [
 ]
 python-dateutil = ">=2.8.2"
 pytz = ">=2020.1"
-tzdata = ">=2022.1"
+tzdata = ">=2022.7"
 
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 [[package]]
 name = "pandocfilters"
@@ -4250,13 +4254,13 @@ test = ["attrs (>=17.4.0)", "azure-datalake-store (>=0.0.30)", "azure-storage-bl
 
 [[package]]
 name = "parse"
-version = "1.20.0"
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 description = "parse() is the opposite of format()"
 optional = false
 python-versions = "*"
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 [[package]]
@@ -4397,28 +4401,28 @@ files = [
 
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 description = "A small Python package for determining appropriate platform-specific dirs, e.g. a \"user data dir\"."
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 python-versions = ">=3.8"
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 python-versions = ">=3.8"
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 [package.extras]
@@ -4561,27 +4565,27 @@ files = [
 
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 python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*, !=3.5.*"
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 ]
 
 [package.dependencies]
@@ -5006,13 +4984,13 @@ xml = ["lxml"]
 
 [[package]]
 name = "pytest"
-version = "7.4.4"
+version = "8.0.0"
 description = "pytest: simple powerful testing with Python"
 optional = false
-python-versions = ">=3.7"
+python-versions = ">=3.8"
 files = [
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 ]
 
 [package.dependencies]
@@ -5020,7 +4998,7 @@ colorama = {version = "*", markers = "sys_platform == \"win32\""}
 exceptiongroup = {version = ">=1.0.0rc8", markers = "python_version < \"3.11\""}
 iniconfig = "*"
 packaging = "*"
-pluggy = ">=0.12,<2.0"
+pluggy = ">=1.3.0,<2.0"
 tomli = {version = ">=1.0.0", markers = "python_version < \"3.11\""}
 
 [package.extras]
@@ -5119,13 +5097,13 @@ sortedcontainers = "*"
 
 [[package]]
 name = "pytz"
-version = "2023.3.post1"
+version = "2023.4"
 description = "World timezone definitions, modern and historical"
 optional = false
 python-versions = "*"
 files = [
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 ]
 
 [[package]]
@@ -5448,13 +5426,13 @@ rdflib-jsonld = "0.6.1"
 
 [[package]]
 name = "recipe-scrapers"
-version = "14.53.0"
+version = "14.54.0"
 description = "Python package, scraping recipes from all over the internet"
 optional = true
 python-versions = ">=3.8"
 files = [
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 ]
 
 [package.dependencies]
@@ -5465,13 +5443,13 @@ requests = ">=2.19.1"
 
 [[package]]
 name = "referencing"
-version = "0.32.1"
+version = "0.33.0"
 description = "JSON Referencing + Python"
 optional = false
 python-versions = ">=3.8"
 files = [
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 ]
 
 [package.dependencies]
@@ -5965,45 +5943,45 @@ tests = ["black (>=23.3.0)", "matplotlib (>=3.3.4)", "mypy (>=1.3)", "numpydoc (
 
 [[package]]
 name = "scipy"
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 python-versions = ">=3.9"
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+
+[package.dependencies]
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 [package.extras]
 dev = ["click", "cython-lint (>=0.12.2)", "doit (>=0.36.0)", "mypy", "pycodestyle", "pydevtool", "rich-click", "ruff", "types-psutil", "typing_extensions"]
 doc = ["jupytext", "matplotlib (>2)", "myst-nb", "numpydoc", "pooch", "pydata-sphinx-theme (==0.9.0)", "sphinx (!=4.1.0)", "sphinx-design (>=0.2.0)"]
-test = ["asv", "gmpy2", "mpmath", "pooch", "pytest", "pytest-cov", "pytest-timeout", "pytest-xdist", "scikit-umfpack", "threadpoolctl"]
+test = ["asv", "gmpy2", "hypothesis", "mpmath", "pooch", "pytest", "pytest-cov", "pytest-timeout", "pytest-xdist", "scikit-umfpack", "threadpoolctl"]
 
 [[package]]
 name = "seaborn"
@@ -6290,23 +6268,23 @@ test = ["cython (>=3.0)", "filelock", "html5lib", "pytest (>=4.6)", "setuptools
 
 [[package]]
 name = "sphinx-autodoc-typehints"
-version = "1.25.2"
+version = "1.25.3"
 description = "Type hints (PEP 484) support for the Sphinx autodoc extension"
 optional = true
 python-versions = ">=3.8"
 files = [
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 [package.dependencies]
-furo = {version = ">=2023.7.26", optional = true, markers = "extra == \"docs\""}
+furo = {version = ">=2023.9.10", optional = true, markers = "extra == \"docs\""}
 sphinx = ">=7.1.2"
 
 [package.extras]
-docs = ["furo (>=2023.7.26)", "sphinx (>=7.1.2)"]
+docs = ["furo (>=2023.9.10)"]
 numpy = ["nptyping (>=2.5)"]
-testing = ["covdefaults (>=2.3)", "coverage (>=7.3)", "diff-cover (>=7.7)", "pytest (>=7.4)", "pytest-cov (>=4.1)", "sphobjinv (>=2.3.1)", "typing-extensions (>=4.7.1)"]
+testing = ["covdefaults (>=2.3)", "coverage (>=7.3.2)", "diff-cover (>=8.0.1)", "pytest (>=7.4.3)", "pytest-cov (>=4.1)", "sphobjinv (>=2.3.1)", "typing-extensions (>=4.8)"]
 
 [[package]]
 name = "sphinx-basic-ng"
@@ -6964,13 +6942,13 @@ files = [
 
 [[package]]
 name = "toolz"
-version = "0.12.0"
+version = "0.12.1"
 description = "List processing tools and functional utilities"
 optional = false
-python-versions = ">=3.5"
+python-versions = ">=3.7"
 files = [
-    {file = "toolz-0.12.0-py3-none-any.whl", hash = "sha256:2059bd4148deb1884bb0eb770a3cde70e7f954cfbbdc2285f1f2de01fd21eb6f"},
-    {file = "toolz-0.12.0.tar.gz", hash = "sha256:88c570861c440ee3f2f6037c4654613228ff40c93a6c25e0eba70d17282c6194"},
+    {file = "toolz-0.12.1-py3-none-any.whl", hash = "sha256:d22731364c07d72eea0a0ad45bafb2c2937ab6fd38a3507bf55eae8744aa7d85"},
+    {file = "toolz-0.12.1.tar.gz", hash = "sha256:ecca342664893f177a13dac0e6b41cbd8ac25a358e5f215316d43e2100224f4d"},
 ]
 
 [[package]]
@@ -7179,13 +7157,13 @@ zstd = ["zstandard (>=0.18.0)"]
 
 [[package]]
 name = "uvicorn"
-version = "0.26.0"
+version = "0.27.0.post1"
 description = "The lightning-fast ASGI server."
 optional = true
 python-versions = ">=3.8"
 files = [
-    {file = "uvicorn-0.26.0-py3-none-any.whl", hash = "sha256:cdb58ef6b8188c6c174994b2b1ba2150a9a8ae7ea5fb2f1b856b94a815d6071d"},
-    {file = "uvicorn-0.26.0.tar.gz", hash = "sha256:48bfd350fce3c5c57af5fb4995fded8fb50da3b4feb543eb18ad7e0d54589602"},
+    {file = "uvicorn-0.27.0.post1-py3-none-any.whl", hash = "sha256:4b85ba02b8a20429b9b205d015cbeb788a12da527f731811b643fd739ef90d5f"},
+    {file = "uvicorn-0.27.0.post1.tar.gz", hash = "sha256:54898fcd80c13ff1cd28bf77b04ec9dbd8ff60c5259b499b4b12bb0917f22907"},
 ]
 
 [package.dependencies]

From 5366c3658fec55772efb15d128fa1aa51c5b64d0 Mon Sep 17 00:00:00 2001
From: caufieldjh <j.harry.caufield@gmail.com>
Date: Wed, 31 Jan 2024 14:22:10 -0500
Subject: [PATCH 2/2] Add basic datascan command - for now this is a clone of
 web-extract using datasheet schema

---
 src/ontogpt/cli.py | 32 ++++++++++++++++++++++++++++++++
 1 file changed, 32 insertions(+)

diff --git a/src/ontogpt/cli.py b/src/ontogpt/cli.py
index 7a786d0f5..e4a8c2ee3 100644
--- a/src/ontogpt/cli.py
+++ b/src/ontogpt/cli.py
@@ -753,6 +753,38 @@ def web_extract(model, template, url, output, output_format, show_prompt, **kwar
     results = ke.extract_from_text(text=text, show_prompt=show_prompt)
     write_extraction(results, output, output_format, ke)
 
+@main.command()
+@model_option
+@recurse_option
+@output_option_wb
+@output_format_options
+@show_prompt_option
+@click.argument("url")
+def datascan(model, url, output, output_format, show_prompt, **kwargs):
+    """Extract knowledge about a dataset from multiple sources."""
+    if not model:
+        model = DEFAULT_MODEL
+    selectmodel = get_model_by_name(model)
+
+    template_details = get_template_details(template="datasheet")
+
+    ke = SPIRESEngine(
+        template_details=template_details,
+        model=selectmodel["canonical_name"],
+        model_source=selectmodel["provider"].lower(),
+        **kwargs,
+    )
+    if settings.cache_db:
+        ke.client.cache_db_path = settings.cache_db
+    if settings.skip_annotators:
+        ke.skip_annotators = settings.skip_annotators
+
+    web_client = SoupClient()
+    text = web_client.text(url)
+
+    logging.debug(f"Input text: {text}")
+    results = ke.extract_from_text(text=text, show_prompt=show_prompt)
+    write_extraction(results, output, output_format, ke)
 
 @main.command()
 @output_option_wb