From be32760b4080ccb500b6f539fbf3304ccb19d17f Mon Sep 17 00:00:00 2001 From: Piyush Yadav Date: Sat, 19 Feb 2022 12:21:37 -0800 Subject: [PATCH 1/5] comment based changes, added ftx for ontologies --- examples/mimic_iii/.DS_Store | Bin 6148 -> 0 bytes .../mimic3_note_reader.cpython-39.pyc | Bin 2463 -> 0 bytes examples/mimic_iii/demo/.generated | 0 .../demo/__pycache__/__init__.cpython-39.pyc | Bin 159 -> 0 bytes .../demo/__pycache__/clinical.cpython-39.pyc | Bin 1839 -> 0 bytes .../ontology_specs/clinical_onto.json | 12 ++--- forte_medical/ontology_specs/demo/.generated | 0 forte_medical/ontology_specs/demo/__init__.py | 1 - .../demo/__pycache__/__init__.cpython-39.pyc | Bin 169 -> 0 bytes .../demo/__pycache__/clinical.cpython-39.pyc | Bin 1849 -> 0 bytes forte_medical/ontology_specs/demo/clinical.py | 49 ------------------ .../mimic3_note_reader.cpython-39.pyc | Bin 2495 -> 0 bytes forte_medical/readers/mimic3_note_reader.py | 2 +- .../demo => ftx/medical}/__init__.py | 0 .../demo => ftx/medical}/clinical.py | 2 +- 15 files changed, 8 insertions(+), 58 deletions(-) delete mode 100644 examples/mimic_iii/.DS_Store delete mode 100644 examples/mimic_iii/__pycache__/mimic3_note_reader.cpython-39.pyc delete mode 100644 examples/mimic_iii/demo/.generated delete mode 100644 examples/mimic_iii/demo/__pycache__/__init__.cpython-39.pyc delete mode 100644 examples/mimic_iii/demo/__pycache__/clinical.cpython-39.pyc delete mode 100644 forte_medical/ontology_specs/demo/.generated delete mode 100644 forte_medical/ontology_specs/demo/__init__.py delete mode 100644 forte_medical/ontology_specs/demo/__pycache__/__init__.cpython-39.pyc delete mode 100644 forte_medical/ontology_specs/demo/__pycache__/clinical.cpython-39.pyc delete mode 100644 forte_medical/ontology_specs/demo/clinical.py delete mode 100644 forte_medical/readers/__pycache__/mimic3_note_reader.cpython-39.pyc rename {examples/mimic_iii/demo => ftx/medical}/__init__.py (100%) rename {examples/mimic_iii/demo => 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packages=setuptools.find_namespace_packages( + include=['ftx.*'], exclude=["scripts*", "examples*", "tests*"] ), install_requires=[ From 521654fce4126fd391e26b21cba026de87abfb69 Mon Sep 17 00:00:00 2001 From: Piyush Yadav Date: Tue, 22 Feb 2022 19:02:22 -0800 Subject: [PATCH 3/5] updated example code with correct namespace --- examples/mimic_iii/medical_pipeline.py | 2 +- ftx/.DS_Store | Bin 0 -> 6148 bytes ftx/medical.py | 0 ftx/medical/.DS_Store | Bin 0 -> 6148 bytes 4 files changed, 1 insertion(+), 1 deletion(-) create mode 100644 ftx/.DS_Store create mode 100644 ftx/medical.py create mode 100644 ftx/medical/.DS_Store diff --git a/examples/mimic_iii/medical_pipeline.py b/examples/mimic_iii/medical_pipeline.py index 3f4d15fb..f8ba047b 100644 --- a/examples/mimic_iii/medical_pipeline.py +++ b/examples/mimic_iii/medical_pipeline.py @@ -5,7 +5,7 @@ from forte.data.readers import StringReader from forte.pipeline import Pipeline from forte.processors.writers import PackIdJsonPackWriter -from ftx.medical import MedicalEntityMention +from ftx.medical.clinical import MedicalEntityMention from ft.onto.base_ontology import ( Token, diff --git a/ftx/.DS_Store b/ftx/.DS_Store new file mode 100644 index 0000000000000000000000000000000000000000..d6e88bd2ea0eade92d96f4642ac6003212941dff GIT binary patch literal 6148 zcmeHKL2uJA6n^f?mQW$}0D=pWC9c&d>jav(gt8sD5(Ec8C21;%$l|I^sZdoZSNJnK z?w{=M!1rty(RQGn5Q6ur=kLXSpWS>;?3jpDf0jKUY7HR<>09jSBGGwd|bbRMOA$_xV|2hG}6^Wbos02H*c?4H2`3RDi*(Ati`; z);Cz{?gnd*PH9BhinB4sliz2j^Xb_Cqw{oJ3dnNnhrp`JjFCsVS=@FGmwg$g>er-n`1o%*^{{R%TPnja@?!hT))n zd$D+Q(9yla-m;??M+e=GKI}bQF2mr~z59=!4?Y&BrTN0j;BCO`VC{y-6?{doA;G73 zQWmCsj}~TKUl-^yQMaaI)w`f5APR^AS5&|+QbFsA`I06IhywqQ0=zzGIAi3oc4(Il z6!r)JY@*s4V*XfUj`kRNtR12SrW_UMsLCHPl%u0w`@G0w?ad3Y^ZtMG>+}CQNv=czQQ)6aKsAr!<34W5@2y)m$9t`Yzk{=J oUhVJ)1%cg)k;_~09k?~rYYu>s$J!xkVDcegWspJ?_@fGZ2P8#-N&o-= literal 0 HcmV?d00001 diff --git a/ftx/medical.py b/ftx/medical.py new file mode 100644 index 00000000..e69de29b diff --git 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b/ftx/medical/.DS_Store deleted file mode 100644 index f94125c4873ac18591a41a8b6c5e65c3eb1d081e..0000000000000000000000000000000000000000 GIT binary patch literal 0 HcmV?d00001 literal 6148 zcmeHK%Sr=55bQBI1ab+UJkA#^_y=Q%2hV;$G%G@6aRWxs+y0TCs8!vqxDW6qBHdxS zdS<$2W(zV85lQRkyK|A1h%8WuiNS=id9v%oljp#sW9;Q9Tl^|HObqlFo4EF+u6Zwy z@_qfUS4~^*ns$c_%5#BIy{jQ2tCj`~vTC_S%@-Uh7G5o;?g#yG-P@*q#F{V?-P z?vej8$QsV1iwqYEgaV;JC=d#a6u_BHTPzL3hXSEMDDb5K_lJx^ERLO_ZXIy?1OW0H zt%jJFWpc7(aqJAy14~8)8a4S7BN-j-+4G8HXJ~Xu{`g2f^XKCw>FgLkYr3Rj7(NsT z1^Noith(a)e~G`$vPpY#n_b&)SS~gF<6o#{h=7cL_j+ g`^cGgT7PDYyyDmyaul{J9T*n@6(n3J@Cyoj01+ugNdN!< diff --git a/ftx/medical/clinical.py b/ftx/medical/clinical.py index 0ddb45e9..db82a90f 100644 --- a/ftx/medical/clinical.py +++ b/ftx/medical/clinical.py @@ -1,5 +1,5 @@ # ***automatically_generated*** -# ***source json:../forte-medical/ftx/medical/clinical_onto.json*** +# ***source json:../../../../casl/forte-medical/forte_medical/ontology_specs/clinical_onto.json*** # flake8: noqa # mypy: ignore-errors # pylint: skip-file From e71c59476a4c9d88672a974ce15c17931d2bf0a4 Mon Sep 17 00:00:00 2001 From: Piyush Yadav Date: Wed, 23 Feb 2022 11:37:06 -0800 Subject: [PATCH 5/5] added a g.gitignore file --- .gitignore | 225 +++++++++++++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 225 insertions(+) create mode 100644 .gitignore diff --git a/.gitignore b/.gitignore new file mode 100644 index 00000000..9df06b8e --- /dev/null +++ b/.gitignore @@ -0,0 +1,225 @@ +# Created by https://www.gitignore.io/api/python + +### Python ### +# Byte-compiled / optimized / DLL files +__pycache__/ +*.py[cod] +*$py.class + +# C extensions +*.so + +# Distribution / packaging +.Python +env/ +build/ +develop-eggs/ +dist/ +downloads/ +eggs/ +.eggs/ +lib/ +lib64/ +parts/ +sdist/ +var/ +wheels/ +*.egg-info/ +.installed.cfg +*.egg + +# PyInstaller +# Usually these files are written by a python script from a template +# before PyInstaller builds the exe, so as to inject date/other infos into it. +*.manifest +*.spec + +# Installer logs +pip-log.txt +pip-delete-this-directory.txt + +# Unit test / coverage reports +htmlcov/ +.tox/ +.coverage +.coverage.* +.cache +nosetests.xml +coverage.xml +*,cover +.hypothesis/ + +# Translations +*.mo +*.pot + +# Django stuff: +*.log +local_settings.py + +# Flask stuff: +instance/ +.webassets-cache + +# Scrapy stuff: +.scrapy + +# Sphinx documentation +docs/_build/ + +# PyBuilder +target/ + +# Jupyter Notebook +.ipynb_checkpoints + +# pyenv +.python-version + +# celery beat schedule file +celerybeat-schedule + +# SageMath parsed files +*.sage.py + +# dotenv +.env + +# virtualenv +.venv +venv/ +ENV/ + +# Spyder project settings +.spyderproject +.spyproject + +# Rope project settings +.ropeproject + +# mkdocs documentation +/site + + +### Linux ### +*~ + +# temporary files which can be created if a process still has a handle open of a deleted file +.fuse_hidden* + +# KDE directory preferences +.directory + +# Linux trash folder which might appear on any partition or disk +.Trash-* + +# .nfs files are created when an open file is removed but is still being accessed +.nfs* + + +### macOS ### +*.DS_Store +.AppleDouble +.LSOverride + +# Icon must end with two \r +Icon + +# Thumbnails +._* + +# Files that might appear in the root of a volume +.DocumentRevisions-V100 +.fseventsd +.Spotlight-V100 +.TemporaryItems +.Trashes +.VolumeIcon.icns +.com.apple.timemachine.donotpresent + +# Directories potentially created on remote AFP share +.AppleDB +.AppleDesktop +Network Trash Folder +Temporary Items +.apdisk + + +### Vim ### +# swap +[._]*.s[a-v][a-z] +[._]*.sw[a-p] +[._]s[a-v][a-z] +[._]sw[a-p] +# session +Session.vim +# temporary +.netrwhist +# auto-generated tag files +tags + + +### Emacs ### +# -*- mode: gitignore; -*- +\#*\# +/.emacs.desktop +/.emacs.desktop.lock +*.elc +auto-save-list +tramp +.\#* + +# Org-mode +.org-id-locations +*_archive + +# flymake-mode +*_flymake.* + +# eshell files +/eshell/history +/eshell/lastdir + +# elpa packages +/elpa/ + +# reftex files +*.rel + +# AUCTeX auto folder +/auto/ + +# cask packages +.cask/ + +# Flycheck +flycheck_*.el + +# server auth directory +/server/ + +# projectiles files +.projectile + +# directory configuration +.dir-locals.el + +# Editors +.idea +.vscode + +docs/_build +.generated + +### IntelliJ ### +*.iml + +### pytest ### +.pytest_cache/ + +### mypy ### +.mypy_cache/ + +### Project ### +en_ewt_models/ +fr_gsd_models/ \ No newline at end of file