cumulus-library

View on PyPIReverse Dependencies (4)

4.1.3 cumulus_library-4.1.3-py3-none-any.whl

Wheel Details

Project: cumulus-library
Version: 4.1.3
Filename: cumulus_library-4.1.3-py3-none-any.whl
Download: [link]
Size: 153575
MD5: ed12832954a013f5fbc5f4382f04aa32
SHA256: d405944947ef5628cf048b26917fbdf02635382eaaa3b7f0f5dd45f85ed63ef3
Uploaded: 2024-12-16 18:48:10 +0000

dist-info

METADATA

Metadata-Version: 2.3
Name: cumulus-library
Version: 4.1.3
Summary: Clinical study SQL generation for data derived from bulk FHIR
Project-Url: Documentation, https://docs.smarthealthit.org/cumulus/library/
Project-Url: Home, https://smarthealthit.org/cumulus/
Project-Url: Source, https://github.com/smart-on-fhir/cumulus-library
Keywords: FHIR,SQL,Health Informatics
Classifier: License :: OSI Approved :: Apache Software License
Classifier: Operating System :: OS Independent
Classifier: Programming Language :: Python :: 3
Classifier: Topic :: Software Development :: Libraries :: Python Modules
Requires-Python: >= 3.11
Requires-Dist: cumulus-fhir-support (>=1.2)
Requires-Dist: duckdb (>=1.1)
Requires-Dist: Jinja2 (>3)
Requires-Dist: pandas (<3,>=2.1.3)
Requires-Dist: psmpy (<1,>=0.3.13)
Requires-Dist: pyarrow (>=11.0)
Requires-Dist: pyathena (>=2.23)
Requires-Dist: pytablewriter (>=1.2)
Requires-Dist: requests (>=2.28)
Requires-Dist: rich (>=13.2)
Requires-Dist: sqlfluff (>=3)
Requires-Dist: sqlparse (>0.4)
Requires-Dist: ruff (<0.9); extra == "dev"
Requires-Dist: pre-commit; extra == "dev"
Requires-Dist: freezegun; extra == "test"
Requires-Dist: pytest; extra == "test"
Requires-Dist: pytest-cov; extra == "test"
Requires-Dist: responses; extra == "test"
Provides-Extra: dev
Provides-Extra: test
Description-Content-Type: text/markdown
[Description omitted; length: 631 characters]

WHEEL

Wheel-Version: 1.0
Generator: flit 3.10.1
Root-Is-Purelib: true
Tag: py3-none-any

RECORD

Path Digest Size
cumulus_library/.sqlfluff sha256=9ueOm8rGpzUeSeoD2vfTArs0l3VEiN1tb05BdbLzH3o 8313
cumulus_library/__init__.py sha256=nRrPbnPxkByUOW3kVxWYrSejRd9N04-DuCRGJtX0Bmc 366
cumulus_library/base_utils.py sha256=7dT9fnD_is-avGQXZ679NKp0vO92Gb3a7_OWWACDMW8 5113
cumulus_library/cli.py sha256=HD0ryiWFwMS9LajuT6UKRO60GMWk-JYosKlNvD9OIxE 18330
cumulus_library/cli_parser.py sha256=0cVn96rjXb4kjhrrHrQeQyeZ8SaLYs_OUXD3qWPyurU 9406
cumulus_library/db_config.py sha256=pdS-GqXk6B7V6oMlg-mjrLS0CCt2DyfqigzAYTmADss 249
cumulus_library/enums.py sha256=G4Cx6agSHqwopmJSYc3clz1-7qdziQizRsLZuZXfflg 729
cumulus_library/errors.py sha256=mt8QI4gjEhldm1Am8ipk-5fQYYfedWVcOTxWmBwF5H8 812
cumulus_library/log_utils.py sha256=ljy4ewCu6vRB5PDSZ7GwDnXhuRA4nm7Cu4Lw0tHMo3c 3660
cumulus_library/module_allowlist.json sha256=G_hNVlUSvdMkFbv_zegvjsNkbIrPx_I0M9nJlTdm4hI 388
cumulus_library/study_manifest.py sha256=EV6u3S6BKBXsmiW3S_Kssj9SeJnHzu1txFQr-EAm6dA 9893
cumulus_library/actions/builder.py sha256=-iekZzgF6uZkrBdjB18jtl0ig_HuBcFXAyt0Dvw-z9A 19835
cumulus_library/actions/cleaner.py sha256=mdwuSgcEWXXr-0LabvHIaxH4Cc3i9uU706c2KE4rJXI 6540
cumulus_library/actions/exporter.py sha256=-qNJEYTI74yH4HPwr4YYngqPsDmmBxp_GiW348j69tg 3735
cumulus_library/actions/file_generator.py sha256=Xc5mywx91ubz6acYZ_VXrRJIFmlq02JO8KHoWfOuirs 3380
cumulus_library/actions/importer.py sha256=O6gM3CM6AOdRAZRsuojFy83ni86tKbsibhEIOp2_9L8 3058
cumulus_library/actions/uploader.py sha256=5FoE1m9ce1Cm15mj3sIyK7cjn-lA_UtfLPa-CqmQwt0 3317
cumulus_library/apis/__init__.py sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU 0
cumulus_library/apis/umls.py sha256=TIgtc57rnWCT7iX9OQv6UoEXHk6dWjBggjlhh2DaSOQ 7557
cumulus_library/builders/README.md sha256=1R2CmB2iHUY3PKAbh5ItmjMjMboQyqIJEujmPRO_1S4 1552
cumulus_library/builders/base_table_builder.py sha256=CiFC0AMJLgqkTp4DHMQ1a-40CmpP-ZNr6vJjUEcZinA 4429
cumulus_library/builders/counts.py sha256=SNQQsI7Ug-SBo-sL-Va84sCAw3Z64s7hfKkIz9xD1tQ 12661
cumulus_library/builders/protected_table_builder.py sha256=ivXzOSXpLuvmCmxOCuDp7xhn6xqJdgkWg5rBSYPyp5k 3130
cumulus_library/builders/psm_builder.py sha256=AxtcxG80ZnhwPtGMVwfUTO4tHjaEXCmtWv5laxmi1-o 14301
cumulus_library/builders/valueset_builder.py sha256=KMwOI90UcVLgiEdMWNufOyFON4laJJ9uiu1eSjKWDRI 2210
cumulus_library/builders/reference_sql/psm.sql sha256=IuAb0h-epv3GVg4Qy2DPqZtSGpDZpIf6KYY_Sp3265s 5136
cumulus_library/builders/statistics_templates/count.sql.jinja sha256=PFY9f6IUzs8DdHVmeoDlHEGvVZsrPMjlggd8VVx3Njg 7581
cumulus_library/builders/statistics_templates/counts_templates.py sha256=yWr02ANGh12RuFxHV23MVwo64a2yRxWTPUfCQphQuHs 2413
cumulus_library/builders/statistics_templates/psm_create_covariate_table.sql.jinja sha256=bQ1VmNqnhhD3OoRaEP3UaxwFnRvBgJI9W9Lt1bZrVtY 1606
cumulus_library/builders/statistics_templates/psm_distinct_ids.sql.jinja sha256=ZW_T9kqAY61gA0J7V2UoZZHPsVnc86qijulKlLFQH5k 355
cumulus_library/builders/statistics_templates/psm_templates.py sha256=077eG0EYi6q3Hk4nfKqplmqgZFMG6eNxpLrfvAshOEQ 3270
cumulus_library/builders/valueset/additional_rules_builder.py sha256=lA28tgiLapnozRyLEo9WiwTy53J-CtLrEq95m7rhGrg 4774
cumulus_library/builders/valueset/lookup_drug_from_ingredient_rules.tsv sha256=mZge4dZwVQX66BnZVkCbI2dcrUEqSB2r5Xfh-WuRTPE 2554
cumulus_library/builders/valueset/rxnorm_valueset_builder.py sha256=Ko3Vh_l_J3jw6LZUMPrSo-m1aDUxMEfyPP8GraKFt2U 5685
cumulus_library/builders/valueset/static_builder.py sha256=OGkKK8mVej4OAlujucFHDT2Fr-qbG9eWD5XbtBGjRqw 8213
cumulus_library/builders/valueset/umls.py sha256=AsPR6pykk9sKpFTkDmHnzg9PjdCeo-oSpIo2GRkiUaU 4541
cumulus_library/builders/valueset/valueset_utils.py sha256=QChixkxLgQN---MhLBbIOme9dg9C5Ba7hFz74XeHHFo 306
cumulus_library/builders/valueset/vsac.py sha256=arNHIfwq-AynHbYPflpjlrSQ18R4j15B5a6Y8NncU14 2808
cumulus_library/builders/valueset/template_sql/create_included_keywords.sql.jinja sha256=drXMpTh-xk1TaqlKRTPM9sODYg8xT90-ExS8UtZjqaA 462
cumulus_library/builders/valueset/template_sql/create_keyword_annotated_table.sql.jinja sha256=P-Pg-HOVS6vQ2HkfPG4Uyot7zudCUp7yDdQ-sWCU3q0 799
cumulus_library/builders/valueset/template_sql/create_search_rules_descriptions.sql.jinja sha256=VEKZGCn5Mo_f23pgx6GcyFN6P2BsVuyYDjkSBHPnTyw 380
cumulus_library/builders/valueset/template_sql/umls_iterate.sql.jinja sha256=KJm7tDFsPM3hqO5SPLEP91Le1HgpMyUEZrp-QPko7KI 1417
cumulus_library/databases/__init__.py sha256=bGPxlVWb91_KMtFXsV3kHGjG7-BmmF0UG-PF4i4e58U 249
cumulus_library/databases/athena.py sha256=qq732MJSWR4i0pDygInLPrgTiZ4IFdItewhHAn7fC0c 8786
cumulus_library/databases/base.py sha256=4NWj1pIg1UtiSFwzoEM_PLIQlbdIjYuPIudSDDlof3I 8138
cumulus_library/databases/duckdb.py sha256=gqcTlRrI_AmErxk1_g0_x_hVDgqKEq6jkJC76IbeeI4 9584
cumulus_library/databases/utils.py sha256=PRXDdDgHB-Y3jX9Kfmi0qD_-54o9zSL9xbIMR7IT5OA 4379
cumulus_library/studies/core/__init__.py sha256=EPmgXOdWKks5S__ZMH7Nu6xpAeVrZpfxaFy4pykuyeI 22
cumulus_library/studies/core/builder_allergyintolerance.py sha256=7MWT57Pnb9byTfHkj1wP1jlNihJfF1EYnd50YSgknk4 2893
cumulus_library/studies/core/builder_condition.py sha256=_JtuHpdtXOxnUmT6E8X1vc-22GpzbQVi3PjhGtOGs7s 3447
cumulus_library/studies/core/builder_diagnosticreport.py sha256=3JPQPyqfpyvVxFJn5WQAxcIPFpBSfDnBA5jJEzjCrkE 1683
cumulus_library/studies/core/builder_documentreference.py sha256=-QfqoM_PDT1wp_woZ-MQ0AIhYYdvOWCZ6_8l-LDskjY 2608
cumulus_library/studies/core/builder_encounter.py sha256=ebZPLVvh9xXnx8pXcCWO2urnx-yMA443dswNdxifRIs 4444
cumulus_library/studies/core/builder_medicationrequest.py sha256=JwZhE0ArB8699UWXAFnxwHC2XEjTVXWDqEVlQ7tlopM 2545
cumulus_library/studies/core/builder_observation.py sha256=RWikXe0Gw0dFpij2YD-YiSzHgfZpzAsbgj_Hm_hQ2Ho 3518
cumulus_library/studies/core/builder_patient.py sha256=Av8WYjBzr72UPN6RGTaFL5ot43Bjh7UDurEgPE1xBJs 2735
cumulus_library/studies/core/builder_prereq_tables.py sha256=MoocSRT9XqxVt3ZQgSJIycvC4hHa1Vp3JaOxLoWSJ8g 809
cumulus_library/studies/core/count_core.py sha256=EyJrl0cvJet27hCKaz1GdDV07ATbY_pV0qHCg7t4DP0 6871
cumulus_library/studies/core/fhir_lookup_tables.sql sha256=Inp_kq5EYCAuzp0VPmVGtumZbbTqv6-64AMgTIrCHAU 948
cumulus_library/studies/core/fhir_mapping_tables.sql sha256=tLFDCVOAOR1eAzqPfy6lKDD4kQEkAQOwTWKsdXZduCU 4879
cumulus_library/studies/core/manifest.toml sha256=VkDgu9fBu41qzUl-cV050In8yV00xjLovkAP0fOMD5g 1031
cumulus_library/studies/core/meta_date.sql sha256=qk_GEnohK3tyG_5t0-3H2qiMpNgEngZ-kzbTiDwkMjI 354
cumulus_library/studies/core/observation_type.sql sha256=Y1EmGby2XmQ7As6TqzZh4K4VkxoBOuL5jXZPWZcLrlk 1694
cumulus_library/studies/core/setup.sql sha256=4yb9awGk0bX7pfV1vvBtmVJ6sB5Ffkhv-Fo-7Ey2EdY 1440
cumulus_library/studies/core/version.sql sha256=YmeI3ElBxOUWWDAiYL4m5E0gdrb8QXaPjnrHYYu89-4 69
cumulus_library/studies/core/core_templates/allergyintolerance.sql.jinja sha256=PX6dpCEkiQVHP_0kNSDnBw_Zz8SL7T84YKQjIhSxueU 4215
cumulus_library/studies/core/core_templates/completion_utils.jinja sha256=8vTaKBdC0gQFP02D8UAk6gvUD4OCClrXkY0P4pQ_pEI 2685
cumulus_library/studies/core/core_templates/condition.sql.jinja sha256=I99a4qcaEXEy8zOuBIAOcOtw433oKFPLT3AEZgFVzxQ 2309
cumulus_library/studies/core/core_templates/core_templates.py sha256=onr5MP2ybO1jTIKZg7tzjPcjxEQCnCvazD-xYrW9qX0 404
cumulus_library/studies/core/core_templates/core_utils.jinja sha256=wXuTv3CpMfn4brduAzHN-GuRlAXdHpiJKA31eDWld7s 4999
cumulus_library/studies/core/core_templates/diagnosticreport.sql.jinja sha256=ruJLLxbYw72BJ7-kOSepVN-lFw_wyk_sJHlH1DtMKeA 4016
cumulus_library/studies/core/core_templates/documentreference.sql.jinja sha256=OXw72mpIUl9iWI9P5_NQmBrOkKmIcukE7QOtwoa3tSM 2743
cumulus_library/studies/core/core_templates/encounter.sql.jinja sha256=rvV-ogJX_I0UJQ53cbkZUFoKY1TQ4deMV0qD0Nne7JM 4646
cumulus_library/studies/core/core_templates/incomplete_encounter.sql.jinja sha256=K6eSB7-HTD77_f00Kc_mQMtf7O9GTqIRnuVAStiSBic 274
cumulus_library/studies/core/core_templates/medicationrequest.sql.jinja sha256=J2T5OaA0MbxoSg0AOq49br_zJ43A0104NqbdC4mz-6I 4344
cumulus_library/studies/core/core_templates/observation.sql.jinja sha256=XRU01Za8Z89mcWUxf5Zv-t0MXg40aSKYeN04aVd0wbI 3125
cumulus_library/studies/core/core_templates/observation_component_valuequantity.sql.jinja sha256=ltrQV4GyPnOHK8ttXzlc7bmNZwza0W3UBI3SXH1zBGw 2065
cumulus_library/studies/core/core_templates/patient.sql.jinja sha256=R00T6V52gZFbPtlModBuB-G2LHKTglC0Uqeom8lvzcI 1854
cumulus_library/studies/core/reference_sql/builder_allergyintolerance.sql sha256=_2vxOngyhhh2uDVnkZ16yWB28riXKTciZ8vZBZiFtKM 8965
cumulus_library/studies/core/reference_sql/builder_condition.sql sha256=9Bia_RgyMrrEW8jdnWFU4Tu9vH5NM-jZfGl0Qwfs_vU 11892
cumulus_library/studies/core/reference_sql/builder_diagnosticreport.sql sha256=T0K7GqzRptLVr3xNO0cYR5aOhYnxZS3242BitO2SRSc 7008
cumulus_library/studies/core/reference_sql/builder_documentreference.sql sha256=_74QqnHuuWIrXjVJjK15WXWDj4gONfybLq9lrV5pvGo 5431
cumulus_library/studies/core/reference_sql/builder_encounter.sql sha256=c8C-hBFagI0_rZnCF-1DOfI-xqRygFe99ib5PgfZbg8 21765
cumulus_library/studies/core/reference_sql/builder_medicationrequest.sql sha256=eL_HsLVKzifYW9S6PjTwJa-bmenLeIUEcov70i432iU 6034
cumulus_library/studies/core/reference_sql/builder_observation.sql sha256=jCBt1uo7cKkGZn8Hpx3pfNn5_e2RI_0sGVCcPCggaXQ 10813
cumulus_library/studies/core/reference_sql/builder_patient.sql sha256=9KTEdS_xf2vhn2PuFlJMTf9d7V2XY0xhrpHqCpic9aw 7061
cumulus_library/studies/core/reference_sql/builder_prereq_tables.sql sha256=qLrACaH9BTdrTST_7YgEjs4LIHQPHUbcoN63YE5yuPg 8008
cumulus_library/studies/core/reference_sql/count_core.sql sha256=CQKtQy2DyzxrXM2eFt__zmfrT4Domp0aIUpZRKKy9Zk 32815
cumulus_library/studies/discovery/__init__.py sha256=J-j-u0itpEFT6irdmWmixQqYMadNl1X91TxUmoiLHMI 22
cumulus_library/studies/discovery/code_definitions.py sha256=yqtGBTPkJEzzKO7gbVOY5xPK3Zd5bTWcC3YhCn88DPY 5335
cumulus_library/studies/discovery/code_detection.py sha256=gjwUhwK4tYMWO9onHEd1A8Fxdi2muP7GxrwL4i_LmnY 2412
cumulus_library/studies/discovery/manifest.toml sha256=Yv0kYCU8caaNlKUYaGiqgK2FZvWHIeCBaQqRNU--ttg 150
cumulus_library/studies/discovery/discovery_templates/code_system_pairs.sql.jinja sha256=iG0-P1rge1H1IPb7QRFKSSKzxaGfGRyoinXl7j_hCBM 1978
cumulus_library/studies/discovery/discovery_templates/discovery_templates.py sha256=KJluFkvs-LZdN8OsXmJRv0M4w5DGP0XM99WjTkLfsyk 1613
cumulus_library/studies/discovery/reference_sql/code_detection.sql sha256=kBVybKTYCoyIFNih1Evqqt-6ol233OCJJIhzw3Oypy0 8625
cumulus_library/template_sql/alias_table.sql.jinja sha256=TIJWT5CPuxUcjKZjE9Kr-NYP5_ZLcjeInUspWIeQGVE 79
cumulus_library/template_sql/base_templates.py sha256=bTQaZi4vaCI4x3Sm_0fXePZWItxrFpWzccC9AstGVUo 17066
cumulus_library/template_sql/codeable_concept_denormalize.sql.jinja sha256=Sl0ef0uEZ8wmJe1jHQxLWKgrVa2feLwHHSLSMxPrZco 4372
cumulus_library/template_sql/coding_denormalize.sql.jinja sha256=Jo1bsGBMXglsQwxCKCN1X96bdFZ4rOenDrzgYi1dVOM 1864
cumulus_library/template_sql/column_datatype.sql.jinja sha256=S8VEiYta6-KYpmB99ro0-1lGcTxasoNoYfDr0Z86Gno 385
cumulus_library/template_sql/create_table_from_tables.sql.jinja sha256=En6S-O4u1817LPbjnkBXRW_LgjDUxv-AYYcXYhvIs5U 542
cumulus_library/template_sql/create_table_from_union.sql.jinja sha256=mZlooDnXkY1n1Zb39ELY4PzdRglu-nQl7I8iH-ixlgc 290
cumulus_library/template_sql/create_view_as.sql.jinja sha256=Wa-qZSaIWCh8_Kflo2A7qMPutJD4gkNuXGbAfJ2a8Uw 563
cumulus_library/template_sql/create_view_from_tables.sql.jinja sha256=WVDA-uyjgdvYMDpwRI6C-E6KyEze0AfoCEdUUSCdgC4 537
cumulus_library/template_sql/ctas.sql.jinja sha256=yVrg_tgMTYGx2yEgMq-ZV4xfcIZielgfZn_oByklE1E 586
cumulus_library/template_sql/ctas_empty.sql.jinja sha256=Wr1p6HK3LE-395Y6YTiZ26uPdE3M070pp5jHrhQ4jdI 544
cumulus_library/template_sql/ctas_from_parquet.sql.jinja sha256=X3obpy70gbG41reOlEXtoQfY6nnex96QHIb_ox9RILk 1001
cumulus_library/template_sql/drop_view_table.sql.jinja sha256=SZzJ_e2i56nqIyicXobJorF4MkOfyv3nw5NZm7Dz1fg 61
cumulus_library/template_sql/extension_denormalize.sql.jinja sha256=Yn9HqqDjifxwnd9EU-B7dRMYeWO79WLLf5HuhMDp2hs 2528
cumulus_library/template_sql/insert_into.sql.jinja sha256=u-zZ42zSopgKdAGOF--mjppIIItCGwfjxOfchaQ6XM0 606
cumulus_library/template_sql/is_table_not_empty.sql.jinja sha256=q1JvCMB40Lf6SOFrvg6SaZ_g9PEQEy4W-lzqccQPIME 439
cumulus_library/template_sql/select_all.sql.jinja sha256=8QgmxCMa9mrkfbcB5ZiJb6eKzOrAQvpy2XVQGfhAS80 34
cumulus_library/template_sql/show_tables.sql.jinja sha256=zlEPyV3qhOcU2h-OPZ_mOQaCdzBjcGnzPbLtHtKDWZw 225
cumulus_library/template_sql/show_views.sql.jinja sha256=u4fcgHZo6DykyA2NX7V6GQmLKluzohn66nDzZibj2dg 220
cumulus_library/template_sql/sql_utils.py sha256=7riwl80Zf8PW0YxQumt79AMdASl2D7NAcMOCfi3cBCA 13769
cumulus_library/template_sql/shared_macros/syntax.sql.jinja sha256=9ThsFn8VjQonS6UpqZAcoBdhqT4wqNzkdktULdpS8aw 2427
cumulus_library/template_sql/shared_macros/unnest_utils.jinja sha256=Ps6Romhdms7v2wXZ2I3YzU6xjJwKl5y2weqy1PTjLFE 1108
cumulus_library-4.1.3.dist-info/entry_points.txt sha256=bQwS4ne_rjJT4Z1ywj812JED-Ox_x9m0iTvUQTgNc84 64
cumulus_library-4.1.3.dist-info/WHEEL sha256=CpUCUxeHQbRN5UGRQHYRJorO5Af-Qy_fHMctcQ8DSGI 82
cumulus_library-4.1.3.dist-info/METADATA sha256=wZZAiKtOyTZTtLchcNQP6Fi4qWWVf6FIKBVZbr22A8g 1977
cumulus_library-4.1.3.dist-info/RECORD

entry_points.txt

cumulus-library = cumulus_library.cli:main_cli