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pyproject.toml
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pyproject.toml
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[tool.poetry]
name = "external-metadata-awareness"
version = "0.1.0"
description = "Tools for fetching and processing external schemas, ontologies and metadata records. Includes value set maintenance."
authors = ["Mark A. Miller <MAM@lbl.gov>"]
readme = "README.md"
[tool.poetry.dependencies]
python = "^3.10"
click = "^8.1.7"
google-cloud-bigquery = "^3.25.0"
llm = "^0.15"
lxml = "^5.3.0"
oaklib = "^0.6.14"
psycopg2-binary = "^2.9.9"
pygithub = "^2.3.0"
pymongo = "^4.8.0"
python-dotenv = "^1.0.1"
tqdm = "^4.66.5"
xmltodict = "^0.13.0"
##python = "^3.10"
#linkml-map = "^0.3.7"
gspread = "^6.1.2"
oauth2client = "^4.1.3"
gsheet-pandas = "^0.2.8"
duckdb = "^1.0.0"
openpyxl = "^3.1.5"
numpy = "2.1.0"
pandas = "^2.2.2"
scikit-learn = "^1.5.1"
scipy = "^1.14.1"
matplotlib = "^3.9.2"
jupyter = "^1.1.1"
pyarrow = "^18.1.0"
[build-system]
requires = ["poetry-core"]
build-backend = "poetry.core.masonry.api"
[tool.poetry.scripts]
biosample-json-to-context-tsv = 'external_metadata_awareness.biosample_json_to_context_tsv:create_biosample_table'
build-prompt-from-template = 'external_metadata_awareness.build_prompt_from_template:process_files'
count-biosample-context-vals-from-postgres = 'external_metadata_awareness.count_biosample_context_vals_from_postgres:main'
detect-curies-in-subset = 'external_metadata_awareness.detect_curies_in_subset:process_tsv'
find-envo-present-no-curie-extracted = 'external_metadata_awareness.find_envo_present_no_curie_extracted:main'
get-extension-unique-slots = 'external_metadata_awareness.get_extension_unique_slots:process_json'
list-mongodb-paths = 'external_metadata_awareness.list_mongodb_paths:main'
load-tsv-into-postgres = 'external_metadata_awareness.load_tsv_into_postgres:load_tsv_to_postgres'
merge-in-reference-data = 'external_metadata_awareness.merge_in_reference_data:process_csvs'
ncbi-packages-csv-report = 'external_metadata_awareness.ncbi_packages_csv_report:xml_to_csv'
normalize-envo-data = 'external_metadata_awareness.normalize_envo_data:main'
or-boolean-columns = 'external_metadata_awareness.or_boolean_columns:process_tsv'
random-sample-resources = 'external_metadata_awareness.random_sample_resources:downsample_json_resources'
sql-to-tsv = 'external_metadata_awareness.sql_to_tsv:run_query'
xml-to-mongo = 'external_metadata_awareness.xml_to_mongo:load_xml_to_mongodb'
#external_metadata_awareness/cborg_test.py
#external_metadata_awareness/dict_print_biosamples_from_efetch.py
#external_metadata_awareness/extract_value_set_evidence.py
#external_metadata_awareness/first_n_attributes_duckdb.py
#external_metadata_awareness/gsheets_helper.py
#external_metadata_awareness/infer_first_committer.py
#external_metadata_awareness/infer_schema_with_batching.py
#external_metadata_awareness/list_public_gcp_bq_databases.py
#external_metadata_awareness/sem_sql_combine.py
#external_metadata_awareness/study-image-table.py