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!! 2023-05-14T06:24:41,888 ******************************************************************************** 2023-05-14T06:24:41,888 ########################################################################## 2023-05-14T06:24:41,888 # configuration would be ignored/result in error due to `pyproject.toml` # 2023-05-14T06:24:41,888 ########################################################################## 2023-05-14T06:24:41,889 The following seems to be defined outside of `pyproject.toml`: 2023-05-14T06:24:41,889 `readme = '[![License: MIT](https://img.shields.io/badge/License-MIT-yellow.svg)](https://opensource.org/licenses/MIT)\n![Build Status](https://github.com/medspacy/medspacy/workflows/medspacy/badge.svg)\n\n# medspacy\nLibrary for clinical NLP with spaCy. \n\n![alt text](./images/medspacy_logo.png "medSpaCy logo")\n\n**MedSpaCy is currently in beta.**\n\n\n# Overview\nMedSpaCy is a library of tools for performing clinical NLP and text processing tasks with the popular [spaCy](https://spacy.io) \nframework. The `medspacy` package brings together a number of other packages, each of which implements specific \nfunctionality for common clinical text processing specific to the clinical domain, such as sentence segmentation, \ncontextual analysis and attribute assertion, and section detection.\n\n`medspacy` is modularized so that each component can be used independently. All of `medspacy` is designed to be used \nas part of a `spacy` processing pipeline. Each of the following modules is available as part of `medspacy`:\n- `medspacy.preprocess`: Destructive preprocessing for modifying clinical text before processing\n- `medspacy.sentence_splitter`: Clinical sentence segmentation\n- `medspacy.ner`: Utilities for extracting concepts from clinical text\n- `medspacy.context`: Implementation of the [ConText](https://www.sciencedirect.com/science/article/pii/S1532046409000744)\nfor detecting semantic modifiers and attributes of entities, including negation and uncertainty\n- `medspacy.section_detection`: Clinical section detection and segmentation\n- `medspacy.postprocess`: Flexible framework for modifying and removing extracted entities\n- `medspacy.io`: Utilities for converting processed texts to structured data and interacting with databases\n- `medspacy.visualization`: Utilities for visualizing concepts and relationships extracted from text\n- `SpacyQuickUMLS`: UMLS concept extraction compatible with spacy and medspacy implemented by [our fork](https://github.com/medspacy/QuickUMLS) of [QuickUMLS](https://github.com/Georgetown-IR-Lab/QuickUMLS). More detail on this component, how to use it, how to generate UMLS resources beyond the small UMLS sample can be found in [this notebook](notebooks/11-QuickUMLS_Extraction.ipynb).\n\nFuture work could include I/O, relations extraction, and pre-trained clinical models.\n\n**As of 10/2/2021 (version 0.2.0.0), medspaCy supports spaCy v3**\n\n# Usage\n## Installation\n\nYou can install `medspacy` using `setup.py`:\n```bash\npython setup.py install\n```\n\nOr with pip:\n```bash\npip install medspacy\n```\n\nTo install a previous version which uses spaCy 2:\n```bash\npip install medspacy==medspacy 0.1.0.2\n```\n\n### Requirements\nThe following packages are required and installed when `medspacy` is installed:\n- spaCy v3\n- [pyrush](https://github.com/medspacy/PyRuSH)\n\nIf you download other models, you can use them by providing the model itself or model name to `medspacy.load(model_name)`:\n```python\nimport spacy; import medspacy\n# Option 1: Load default\nnlp = medspacy.load()\n\n# Option 2: Load from existing model\nnlp = spacy.load("en_core_web_sm", disable={"ner"})\nnlp = medspacy.load(nlp)\n\n# Option 3: Load from model name\nnlp = medspacy.load("en_core_web_sm", disable={"ner"})\n```\n \n## Basic Usage\nHere is a simple example showing how to implement and visualize a simple rule-based pipeline using `medspacy`:\n```python\nimport medspacy\nfrom medspacy.ner import TargetRule\nfrom medspacy.visualization import visualize_ent\n\n# Load medspacy model\nnlp = medspacy.load()\nprint(nlp.pipe_names)\n\ntext = """\nPast Medical History:\n1. Atrial fibrillation\n2. Type II Diabetes Mellitus\n\nAssessment and Plan:\nThere is no evidence of pneumonia. Continue warfarin for Afib. Follow up for management of type 2 DM.\n"""\n\n# Add rules for target concept extraction\ntarget_matcher = nlp.get_pipe("medspacy_target_matcher")\ntarget_rules = [\n TargetRule("atrial fibrillation", "PROBLEM"),\n TargetRule("atrial fibrillation", "PROBLEM", pattern=[{"LOWER": "afib"}]),\n TargetRule("pneumonia", "PROBLEM"),\n TargetRule("Type II Diabetes Mellitus", "PROBLEM", \n pattern=[\n {"LOWER": "type"},\n {"LOWER": {"IN": ["2", "ii", "two"]}},\n {"LOWER": {"IN": ["dm", "diabetes"]}},\n {"LOWER": "mellitus", "OP": "?"}\n ]),\n TargetRule("warfarin", "MEDICATION")\n]\ntarget_matcher.add(target_rules)\n\ndoc = nlp(text)\nvisualize_ent(doc)\n```\n\n`Output:`\n![alt text](./images/simple_text_visualization.png "Example of clinical text processed by medSpaCy")\n\nFor more detailed examples and explanations of each component, see the [notebooks](./notebooks) folder.\n\n# Citing medspaCy\nIf you use medspaCy in your work, consider citing our paper! Presented at the AMIA Annual Symposium 2021, [preprint available on Arxiv](http://arxiv.org/abs/2106.07799).\n\n```\nH. Eyre, A.B. Chapman, K.S. Peterson, J. Shi, P.R. Alba, M.M. Jones, T.L. Box, S.L. DuVall, O. V Patterson,\nLaunching into clinical space with medspaCy: a new clinical text processing toolkit in Python,\nAMIA Annu. Symp. Proc. 2021 (in Press. (n.d.). \nhttp://arxiv.org/abs/2106.07799.\n```\n\n```\n@Article{medspacy,\n Author="Eyre, H. and Chapman, A. B. and Peterson, K. S. and Shi, J. and Alba, P. R. and Jones, M. M. and Box, T. L. and DuVall, S. L. and Patterson, O. V. ",\n Title="{{L}aunching into clinical space with medspa{C}y: a new clinical text processing toolkit in {P}ython}",\n Journal="AMIA Annu Symp Proc",\n Year="2021",\n Volume="2021",\n Pages="438--447"\n}\n\n}\n```\n\n# Made with medSpaCy\nHere are some links to projects or tutorials which use medSpacy. If you have a project which uses medSpaCy which you\'d like to use, let us know!\n- [VA_COVID-19_NLP_BSV](https://github.com/abchapman93/VA_COVID-19_NLP_BSV): An NLP pipeline for [identifying positive cases of COVID-19](https://aclanthology.org/2020.nlpcovid19-acl.10/) from clinical text. Deployed as part of the Department of Veterans Affairs response to COVID-19\n- [clinspacy](https://ml4lhs.github.io/clinspacy/index.html): An R wrapper for spaCy, sciSpaCy, and medSpaCy for performing clinical NLP and UMLS linking in R\n- [mimic34md2020_materials](https://github.com/Melbourne-BMDS/mimic34md2020_materials): A crash course in clinical data science from the University of Melbourne. For medSpaCy materials, see `notebooks/nlp-*.ipynb`\n- [ReHouSED NLP](https://github.com/abchapman93/ReHouSED): An NLP pipeline for [studying Veteran housing stability](https://www.sciencedirect.com/science/article/pii/S153204642100232X) and distinguishing between Veterans who are currently unstably housed and those who have exited homelessness\n'` 2023-05-14T06:24:41,889 According to the spec (see the link below), however, setuptools CANNOT 2023-05-14T06:24:41,889 consider this value unless `readme` is listed as `dynamic`. 2023-05-14T06:24:41,890 https://packaging.python.org/en/latest/specifications/declaring-project-metadata/ 2023-05-14T06:24:41,890 For the time being, `setuptools` will still consider the given value (as a 2023-05-14T06:24:41,890 **transitional** measure), but please note that future releases of setuptools will 2023-05-14T06:24:41,890 follow strictly the standard. 2023-05-14T06:24:41,890 To prevent this warning, you can list `readme` under `dynamic` or alternatively 2023-05-14T06:24:41,891 remove the `[project]` table from your file and rely entirely on other means of 2023-05-14T06:24:41,891 configuration. 2023-05-14T06:24:41,891 By 2023-Oct-30, you need to update your project and remove deprecated calls 2023-05-14T06:24:41,891 or your builds will no longer be supported. 2023-05-14T06:24:41,891 ******************************************************************************** 2023-05-14T06:24:41,891 !! 2023-05-14T06:24:41,892 _handle_missing_dynamic(dist, project_table) 2023-05-14T06:24:41,892 /tmp/pip-build-env-mc50gxxd/overlay/lib/python3.9/site-packages/setuptools/config/_apply_pyprojecttoml.py:69: SetuptoolsWarning: `install_requires` overwritten in `pyproject.toml` (dependencies) 2023-05-14T06:24:41,892 corresp(dist, value, root_dir) 2023-05-14T06:24:42,217 running egg_info 2023-05-14T06:24:42,224 writing medspacy.egg-info/PKG-INFO 2023-05-14T06:24:42,227 writing dependency_links to medspacy.egg-info/dependency_links.txt 2023-05-14T06:24:42,229 writing requirements to medspacy.egg-info/requires.txt 2023-05-14T06:24:42,230 writing top-level names to medspacy.egg-info/top_level.txt 2023-05-14T06:24:42,290 listing git files failed - pretending there aren't any 2023-05-14T06:24:42,298 reading manifest file 'medspacy.egg-info/SOURCES.txt' 2023-05-14T06:24:42,304 adding license file 'LICENSE' 2023-05-14T06:24:42,313 writing manifest file 'medspacy.egg-info/SOURCES.txt' 2023-05-14T06:24:42,427 Getting requirements to build wheel: finished with status 'done' 2023-05-14T06:24:42,438 Created temporary directory: /tmp/pip-modern-metadata-hhtifmp4 2023-05-14T06:24:42,440 Preparing metadata (pyproject.toml): started 2023-05-14T06:24:42,441 Running command Preparing metadata (pyproject.toml) 2023-05-14T06:24:43,013 /tmp/pip-build-env-mc50gxxd/overlay/lib/python3.9/site-packages/setuptools/config/pyprojecttoml.py:66: _BetaConfiguration: Support for `[tool.setuptools]` in `pyproject.toml` is still *beta*. 2023-05-14T06:24:43,014 config = read_configuration(filepath, True, ignore_option_errors, dist) 2023-05-14T06:24:43,051 /tmp/pip-build-env-mc50gxxd/overlay/lib/python3.9/site-packages/setuptools/config/_apply_pyprojecttoml.py:62: _WouldIgnoreField: `readme` defined outside of `pyproject.toml` would be ignored. 2023-05-14T06:24:43,051 !! 2023-05-14T06:24:43,051 ******************************************************************************** 2023-05-14T06:24:43,052 ########################################################################## 2023-05-14T06:24:43,052 # configuration would be ignored/result in error due to `pyproject.toml` # 2023-05-14T06:24:43,052 ########################################################################## 2023-05-14T06:24:43,052 The following seems to be defined outside of `pyproject.toml`: 2023-05-14T06:24:43,053 `readme = '[![License: MIT](https://img.shields.io/badge/License-MIT-yellow.svg)](https://opensource.org/licenses/MIT)\n![Build Status](https://github.com/medspacy/medspacy/workflows/medspacy/badge.svg)\n\n# medspacy\nLibrary for clinical NLP with spaCy. \n\n![alt text](./images/medspacy_logo.png "medSpaCy logo")\n\n**MedSpaCy is currently in beta.**\n\n\n# Overview\nMedSpaCy is a library of tools for performing clinical NLP and text processing tasks with the popular [spaCy](https://spacy.io) \nframework. The `medspacy` package brings together a number of other packages, each of which implements specific \nfunctionality for common clinical text processing specific to the clinical domain, such as sentence segmentation, \ncontextual analysis and attribute assertion, and section detection.\n\n`medspacy` is modularized so that each component can be used independently. All of `medspacy` is designed to be used \nas part of a `spacy` processing pipeline. Each of the following modules is available as part of `medspacy`:\n- `medspacy.preprocess`: Destructive preprocessing for modifying clinical text before processing\n- `medspacy.sentence_splitter`: Clinical sentence segmentation\n- `medspacy.ner`: Utilities for extracting concepts from clinical text\n- `medspacy.context`: Implementation of the [ConText](https://www.sciencedirect.com/science/article/pii/S1532046409000744)\nfor detecting semantic modifiers and attributes of entities, including negation and uncertainty\n- `medspacy.section_detection`: Clinical section detection and segmentation\n- `medspacy.postprocess`: Flexible framework for modifying and removing extracted entities\n- `medspacy.io`: Utilities for converting processed texts to structured data and interacting with databases\n- `medspacy.visualization`: Utilities for visualizing concepts and relationships extracted from text\n- `SpacyQuickUMLS`: UMLS concept extraction compatible with spacy and medspacy implemented by [our fork](https://github.com/medspacy/QuickUMLS) of [QuickUMLS](https://github.com/Georgetown-IR-Lab/QuickUMLS). More detail on this component, how to use it, how to generate UMLS resources beyond the small UMLS sample can be found in [this notebook](notebooks/11-QuickUMLS_Extraction.ipynb).\n\nFuture work could include I/O, relations extraction, and pre-trained clinical models.\n\n**As of 10/2/2021 (version 0.2.0.0), medspaCy supports spaCy v3**\n\n# Usage\n## Installation\n\nYou can install `medspacy` using `setup.py`:\n```bash\npython setup.py install\n```\n\nOr with pip:\n```bash\npip install medspacy\n```\n\nTo install a previous version which uses spaCy 2:\n```bash\npip install medspacy==medspacy 0.1.0.2\n```\n\n### Requirements\nThe following packages are required and installed when `medspacy` is installed:\n- spaCy v3\n- [pyrush](https://github.com/medspacy/PyRuSH)\n\nIf you download other models, you can use them by providing the model itself or model name to `medspacy.load(model_name)`:\n```python\nimport spacy; import medspacy\n# Option 1: Load default\nnlp = medspacy.load()\n\n# Option 2: Load from existing model\nnlp = spacy.load("en_core_web_sm", disable={"ner"})\nnlp = medspacy.load(nlp)\n\n# Option 3: Load from model name\nnlp = medspacy.load("en_core_web_sm", disable={"ner"})\n```\n \n## Basic Usage\nHere is a simple example showing how to implement and visualize a simple rule-based pipeline using `medspacy`:\n```python\nimport medspacy\nfrom medspacy.ner import TargetRule\nfrom medspacy.visualization import visualize_ent\n\n# Load medspacy model\nnlp = medspacy.load()\nprint(nlp.pipe_names)\n\ntext = """\nPast Medical History:\n1. Atrial fibrillation\n2. Type II Diabetes Mellitus\n\nAssessment and Plan:\nThere is no evidence of pneumonia. Continue warfarin for Afib. Follow up for management of type 2 DM.\n"""\n\n# Add rules for target concept extraction\ntarget_matcher = nlp.get_pipe("medspacy_target_matcher")\ntarget_rules = [\n TargetRule("atrial fibrillation", "PROBLEM"),\n TargetRule("atrial fibrillation", "PROBLEM", pattern=[{"LOWER": "afib"}]),\n TargetRule("pneumonia", "PROBLEM"),\n TargetRule("Type II Diabetes Mellitus", "PROBLEM", \n pattern=[\n {"LOWER": "type"},\n {"LOWER": {"IN": ["2", "ii", "two"]}},\n {"LOWER": {"IN": ["dm", "diabetes"]}},\n {"LOWER": "mellitus", "OP": "?"}\n ]),\n TargetRule("warfarin", "MEDICATION")\n]\ntarget_matcher.add(target_rules)\n\ndoc = nlp(text)\nvisualize_ent(doc)\n```\n\n`Output:`\n![alt text](./images/simple_text_visualization.png "Example of clinical text processed by medSpaCy")\n\nFor more detailed examples and explanations of each component, see the [notebooks](./notebooks) folder.\n\n# Citing medspaCy\nIf you use medspaCy in your work, consider citing our paper! Presented at the AMIA Annual Symposium 2021, [preprint available on Arxiv](http://arxiv.org/abs/2106.07799).\n\n```\nH. Eyre, A.B. Chapman, K.S. Peterson, J. Shi, P.R. Alba, M.M. Jones, T.L. Box, S.L. DuVall, O. V Patterson,\nLaunching into clinical space with medspaCy: a new clinical text processing toolkit in Python,\nAMIA Annu. Symp. Proc. 2021 (in Press. (n.d.). \nhttp://arxiv.org/abs/2106.07799.\n```\n\n```\n@Article{medspacy,\n Author="Eyre, H. and Chapman, A. B. and Peterson, K. S. and Shi, J. and Alba, P. R. and Jones, M. M. and Box, T. L. and DuVall, S. L. and Patterson, O. V. ",\n Title="{{L}aunching into clinical space with medspa{C}y: a new clinical text processing toolkit in {P}ython}",\n Journal="AMIA Annu Symp Proc",\n Year="2021",\n Volume="2021",\n Pages="438--447"\n}\n\n}\n```\n\n# Made with medSpaCy\nHere are some links to projects or tutorials which use medSpacy. If you have a project which uses medSpaCy which you\'d like to use, let us know!\n- [VA_COVID-19_NLP_BSV](https://github.com/abchapman93/VA_COVID-19_NLP_BSV): An NLP pipeline for [identifying positive cases of COVID-19](https://aclanthology.org/2020.nlpcovid19-acl.10/) from clinical text. Deployed as part of the Department of Veterans Affairs response to COVID-19\n- [clinspacy](https://ml4lhs.github.io/clinspacy/index.html): An R wrapper for spaCy, sciSpaCy, and medSpaCy for performing clinical NLP and UMLS linking in R\n- [mimic34md2020_materials](https://github.com/Melbourne-BMDS/mimic34md2020_materials): A crash course in clinical data science from the University of Melbourne. For medSpaCy materials, see `notebooks/nlp-*.ipynb`\n- [ReHouSED NLP](https://github.com/abchapman93/ReHouSED): An NLP pipeline for [studying Veteran housing stability](https://www.sciencedirect.com/science/article/pii/S153204642100232X) and distinguishing between Veterans who are currently unstably housed and those who have exited homelessness\n'` 2023-05-14T06:24:43,053 According to the spec (see the link below), however, setuptools CANNOT 2023-05-14T06:24:43,053 consider this value unless `readme` is listed as `dynamic`. 2023-05-14T06:24:43,053 https://packaging.python.org/en/latest/specifications/declaring-project-metadata/ 2023-05-14T06:24:43,054 For the time being, `setuptools` will still consider the given value (as a 2023-05-14T06:24:43,054 **transitional** measure), but please note that future releases of setuptools will 2023-05-14T06:24:43,054 follow strictly the standard. 2023-05-14T06:24:43,054 To prevent this warning, you can list `readme` under `dynamic` or alternatively 2023-05-14T06:24:43,054 remove the `[project]` table from your file and rely entirely on other means of 2023-05-14T06:24:43,054 configuration. 2023-05-14T06:24:43,055 By 2023-Oct-30, you need to update your project and remove deprecated calls 2023-05-14T06:24:43,055 or your builds will no longer be supported. 2023-05-14T06:24:43,055 ******************************************************************************** 2023-05-14T06:24:43,055 !! 2023-05-14T06:24:43,055 _handle_missing_dynamic(dist, project_table) 2023-05-14T06:24:43,055 /tmp/pip-build-env-mc50gxxd/overlay/lib/python3.9/site-packages/setuptools/config/_apply_pyprojecttoml.py:69: SetuptoolsWarning: `install_requires` overwritten in `pyproject.toml` (dependencies) 2023-05-14T06:24:43,056 corresp(dist, value, root_dir) 2023-05-14T06:24:43,356 running dist_info 2023-05-14T06:24:43,363 creating /tmp/pip-modern-metadata-hhtifmp4/medspacy.egg-info 2023-05-14T06:24:43,369 writing /tmp/pip-modern-metadata-hhtifmp4/medspacy.egg-info/PKG-INFO 2023-05-14T06:24:43,372 writing dependency_links to /tmp/pip-modern-metadata-hhtifmp4/medspacy.egg-info/dependency_links.txt 2023-05-14T06:24:43,375 writing requirements to /tmp/pip-modern-metadata-hhtifmp4/medspacy.egg-info/requires.txt 2023-05-14T06:24:43,376 writing top-level names to /tmp/pip-modern-metadata-hhtifmp4/medspacy.egg-info/top_level.txt 2023-05-14T06:24:43,378 writing manifest file '/tmp/pip-modern-metadata-hhtifmp4/medspacy.egg-info/SOURCES.txt' 2023-05-14T06:24:43,434 listing git files failed - pretending there aren't any 2023-05-14T06:24:43,441 reading manifest file '/tmp/pip-modern-metadata-hhtifmp4/medspacy.egg-info/SOURCES.txt' 2023-05-14T06:24:43,445 adding license file 'LICENSE' 2023-05-14T06:24:43,452 writing manifest file '/tmp/pip-modern-metadata-hhtifmp4/medspacy.egg-info/SOURCES.txt' 2023-05-14T06:24:43,453 creating '/tmp/pip-modern-metadata-hhtifmp4/medspacy-1.1.1a0.dist-info' 2023-05-14T06:24:43,604 Preparing metadata (pyproject.toml): finished with status 'done' 2023-05-14T06:24:43,611 Source in /tmp/pip-wheel-fsqc0ni0/medspacy_2a035781a93a40ea9bb2976488c069f4 has version 1.1.1a0, which satisfies requirement medspacy==1.1.1a0 from https://files.pythonhosted.org/packages/4f/fa/07558929a3d8602d3a16b5b9e8dbf934e578ee657005cc194cac19344451/medspacy-1.1.1a0.tar.gz 2023-05-14T06:24:43,612 Removed medspacy==1.1.1a0 from https://files.pythonhosted.org/packages/4f/fa/07558929a3d8602d3a16b5b9e8dbf934e578ee657005cc194cac19344451/medspacy-1.1.1a0.tar.gz from build tracker '/tmp/pip-build-tracker-8nq79i5y' 2023-05-14T06:24:43,620 Created temporary directory: /tmp/pip-unpack-melkth6f 2023-05-14T06:24:43,620 Building wheels for collected packages: medspacy 2023-05-14T06:24:43,625 Created temporary directory: /tmp/pip-wheel-b3mk8ui0 2023-05-14T06:24:43,625 Destination directory: /tmp/pip-wheel-b3mk8ui0 2023-05-14T06:24:43,627 Building wheel for medspacy (pyproject.toml): started 2023-05-14T06:24:43,628 Running command Building wheel for medspacy (pyproject.toml) 2023-05-14T06:24:44,169 /tmp/pip-build-env-mc50gxxd/overlay/lib/python3.9/site-packages/setuptools/config/pyprojecttoml.py:66: _BetaConfiguration: Support for `[tool.setuptools]` in `pyproject.toml` is still *beta*. 2023-05-14T06:24:44,169 config = read_configuration(filepath, True, ignore_option_errors, dist) 2023-05-14T06:24:44,203 /tmp/pip-build-env-mc50gxxd/overlay/lib/python3.9/site-packages/setuptools/config/_apply_pyprojecttoml.py:62: _WouldIgnoreField: `readme` defined outside of `pyproject.toml` would be ignored. 2023-05-14T06:24:44,204 !! 2023-05-14T06:24:44,204 ******************************************************************************** 2023-05-14T06:24:44,204 ########################################################################## 2023-05-14T06:24:44,204 # configuration would be ignored/result in error due to `pyproject.toml` # 2023-05-14T06:24:44,204 ########################################################################## 2023-05-14T06:24:44,205 The following seems to be defined outside of `pyproject.toml`: 2023-05-14T06:24:44,205 `readme = '[![License: MIT](https://img.shields.io/badge/License-MIT-yellow.svg)](https://opensource.org/licenses/MIT)\n![Build Status](https://github.com/medspacy/medspacy/workflows/medspacy/badge.svg)\n\n# medspacy\nLibrary for clinical NLP with spaCy. \n\n![alt text](./images/medspacy_logo.png "medSpaCy logo")\n\n**MedSpaCy is currently in beta.**\n\n\n# Overview\nMedSpaCy is a library of tools for performing clinical NLP and text processing tasks with the popular [spaCy](https://spacy.io) \nframework. The `medspacy` package brings together a number of other packages, each of which implements specific \nfunctionality for common clinical text processing specific to the clinical domain, such as sentence segmentation, \ncontextual analysis and attribute assertion, and section detection.\n\n`medspacy` is modularized so that each component can be used independently. All of `medspacy` is designed to be used \nas part of a `spacy` processing pipeline. Each of the following modules is available as part of `medspacy`:\n- `medspacy.preprocess`: Destructive preprocessing for modifying clinical text before processing\n- `medspacy.sentence_splitter`: Clinical sentence segmentation\n- `medspacy.ner`: Utilities for extracting concepts from clinical text\n- `medspacy.context`: Implementation of the [ConText](https://www.sciencedirect.com/science/article/pii/S1532046409000744)\nfor detecting semantic modifiers and attributes of entities, including negation and uncertainty\n- `medspacy.section_detection`: Clinical section detection and segmentation\n- `medspacy.postprocess`: Flexible framework for modifying and removing extracted entities\n- `medspacy.io`: Utilities for converting processed texts to structured data and interacting with databases\n- `medspacy.visualization`: Utilities for visualizing concepts and relationships extracted from text\n- `SpacyQuickUMLS`: UMLS concept extraction compatible with spacy and medspacy implemented by [our fork](https://github.com/medspacy/QuickUMLS) of [QuickUMLS](https://github.com/Georgetown-IR-Lab/QuickUMLS). More detail on this component, how to use it, how to generate UMLS resources beyond the small UMLS sample can be found in [this notebook](notebooks/11-QuickUMLS_Extraction.ipynb).\n\nFuture work could include I/O, relations extraction, and pre-trained clinical models.\n\n**As of 10/2/2021 (version 0.2.0.0), medspaCy supports spaCy v3**\n\n# Usage\n## Installation\n\nYou can install `medspacy` using `setup.py`:\n```bash\npython setup.py install\n```\n\nOr with pip:\n```bash\npip install medspacy\n```\n\nTo install a previous version which uses spaCy 2:\n```bash\npip install medspacy==medspacy 0.1.0.2\n```\n\n### Requirements\nThe following packages are required and installed when `medspacy` is installed:\n- spaCy v3\n- [pyrush](https://github.com/medspacy/PyRuSH)\n\nIf you download other models, you can use them by providing the model itself or model name to `medspacy.load(model_name)`:\n```python\nimport spacy; import medspacy\n# Option 1: Load default\nnlp = medspacy.load()\n\n# Option 2: Load from existing model\nnlp = spacy.load("en_core_web_sm", disable={"ner"})\nnlp = medspacy.load(nlp)\n\n# Option 3: Load from model name\nnlp = medspacy.load("en_core_web_sm", disable={"ner"})\n```\n \n## Basic Usage\nHere is a simple example showing how to implement and visualize a simple rule-based pipeline using `medspacy`:\n```python\nimport medspacy\nfrom medspacy.ner import TargetRule\nfrom medspacy.visualization import visualize_ent\n\n# Load medspacy model\nnlp = medspacy.load()\nprint(nlp.pipe_names)\n\ntext = """\nPast Medical History:\n1. Atrial fibrillation\n2. Type II Diabetes Mellitus\n\nAssessment and Plan:\nThere is no evidence of pneumonia. Continue warfarin for Afib. Follow up for management of type 2 DM.\n"""\n\n# Add rules for target concept extraction\ntarget_matcher = nlp.get_pipe("medspacy_target_matcher")\ntarget_rules = [\n TargetRule("atrial fibrillation", "PROBLEM"),\n TargetRule("atrial fibrillation", "PROBLEM", pattern=[{"LOWER": "afib"}]),\n TargetRule("pneumonia", "PROBLEM"),\n TargetRule("Type II Diabetes Mellitus", "PROBLEM", \n pattern=[\n {"LOWER": "type"},\n {"LOWER": {"IN": ["2", "ii", "two"]}},\n {"LOWER": {"IN": ["dm", "diabetes"]}},\n {"LOWER": "mellitus", "OP": "?"}\n ]),\n TargetRule("warfarin", "MEDICATION")\n]\ntarget_matcher.add(target_rules)\n\ndoc = nlp(text)\nvisualize_ent(doc)\n```\n\n`Output:`\n![alt text](./images/simple_text_visualization.png "Example of clinical text processed by medSpaCy")\n\nFor more detailed examples and explanations of each component, see the [notebooks](./notebooks) folder.\n\n# Citing medspaCy\nIf you use medspaCy in your work, consider citing our paper! Presented at the AMIA Annual Symposium 2021, [preprint available on Arxiv](http://arxiv.org/abs/2106.07799).\n\n```\nH. Eyre, A.B. Chapman, K.S. Peterson, J. Shi, P.R. Alba, M.M. Jones, T.L. Box, S.L. DuVall, O. V Patterson,\nLaunching into clinical space with medspaCy: a new clinical text processing toolkit in Python,\nAMIA Annu. Symp. Proc. 2021 (in Press. (n.d.). \nhttp://arxiv.org/abs/2106.07799.\n```\n\n```\n@Article{medspacy,\n Author="Eyre, H. and Chapman, A. B. and Peterson, K. S. and Shi, J. and Alba, P. R. and Jones, M. M. and Box, T. L. and DuVall, S. L. and Patterson, O. V. ",\n Title="{{L}aunching into clinical space with medspa{C}y: a new clinical text processing toolkit in {P}ython}",\n Journal="AMIA Annu Symp Proc",\n Year="2021",\n Volume="2021",\n Pages="438--447"\n}\n\n}\n```\n\n# Made with medSpaCy\nHere are some links to projects or tutorials which use medSpacy. If you have a project which uses medSpaCy which you\'d like to use, let us know!\n- [VA_COVID-19_NLP_BSV](https://github.com/abchapman93/VA_COVID-19_NLP_BSV): An NLP pipeline for [identifying positive cases of COVID-19](https://aclanthology.org/2020.nlpcovid19-acl.10/) from clinical text. Deployed as part of the Department of Veterans Affairs response to COVID-19\n- [clinspacy](https://ml4lhs.github.io/clinspacy/index.html): An R wrapper for spaCy, sciSpaCy, and medSpaCy for performing clinical NLP and UMLS linking in R\n- [mimic34md2020_materials](https://github.com/Melbourne-BMDS/mimic34md2020_materials): A crash course in clinical data science from the University of Melbourne. For medSpaCy materials, see `notebooks/nlp-*.ipynb`\n- [ReHouSED NLP](https://github.com/abchapman93/ReHouSED): An NLP pipeline for [studying Veteran housing stability](https://www.sciencedirect.com/science/article/pii/S153204642100232X) and distinguishing between Veterans who are currently unstably housed and those who have exited homelessness\n'` 2023-05-14T06:24:44,205 According to the spec (see the link below), however, setuptools CANNOT 2023-05-14T06:24:44,205 consider this value unless `readme` is listed as `dynamic`. 2023-05-14T06:24:44,206 https://packaging.python.org/en/latest/specifications/declaring-project-metadata/ 2023-05-14T06:24:44,206 For the time being, `setuptools` will still consider the given value (as a 2023-05-14T06:24:44,206 **transitional** measure), but please note that future releases of setuptools will 2023-05-14T06:24:44,206 follow strictly the standard. 2023-05-14T06:24:44,207 To prevent this warning, you can list `readme` under `dynamic` or alternatively 2023-05-14T06:24:44,207 remove the `[project]` table from your file and rely entirely on other means of 2023-05-14T06:24:44,207 configuration. 2023-05-14T06:24:44,207 By 2023-Oct-30, you need to update your project and remove deprecated calls 2023-05-14T06:24:44,207 or your builds will no longer be supported. 2023-05-14T06:24:44,207 ******************************************************************************** 2023-05-14T06:24:44,208 !! 2023-05-14T06:24:44,208 _handle_missing_dynamic(dist, project_table) 2023-05-14T06:24:44,208 /tmp/pip-build-env-mc50gxxd/overlay/lib/python3.9/site-packages/setuptools/config/_apply_pyprojecttoml.py:69: SetuptoolsWarning: `install_requires` overwritten in `pyproject.toml` (dependencies) 2023-05-14T06:24:44,208 corresp(dist, value, root_dir) 2023-05-14T06:24:44,491 running bdist_wheel 2023-05-14T06:24:44,513 running build 2023-05-14T06:24:44,513 running build_py 2023-05-14T06:24:44,521 creating build 2023-05-14T06:24:44,521 creating build/lib 2023-05-14T06:24:44,522 creating build/lib/medspacy 2023-05-14T06:24:44,523 copying medspacy/ner.py -> build/lib/medspacy 2023-05-14T06:24:44,525 copying medspacy/_version.py -> build/lib/medspacy 2023-05-14T06:24:44,527 copying medspacy/visualization.py -> build/lib/medspacy 2023-05-14T06:24:44,529 copying medspacy/sentence_splitting.py -> build/lib/medspacy 2023-05-14T06:24:44,531 copying medspacy/__init__.py -> build/lib/medspacy 2023-05-14T06:24:44,532 copying medspacy/util.py -> build/lib/medspacy 2023-05-14T06:24:44,535 copying medspacy/components.py -> build/lib/medspacy 2023-05-14T06:24:44,536 copying medspacy/custom_tokenizer.py -> build/lib/medspacy 2023-05-14T06:24:44,538 copying medspacy/_extensions.py -> build/lib/medspacy 2023-05-14T06:24:44,541 creating build/lib/tests 2023-05-14T06:24:44,542 copying tests/test_medspacy.py -> build/lib/tests 2023-05-14T06:24:44,544 copying tests/__init__.py -> build/lib/tests 2023-05-14T06:24:44,546 copying tests/test_extensions.py -> build/lib/tests 2023-05-14T06:24:44,548 copying tests/test_notebooks.py -> build/lib/tests 2023-05-14T06:24:44,550 creating build/lib/medspacy/postprocess 2023-05-14T06:24:44,551 copying medspacy/postprocess/postprocessor.py -> build/lib/medspacy/postprocess 2023-05-14T06:24:44,553 copying medspacy/postprocess/postprocessing_functions.py -> build/lib/medspacy/postprocess 2023-05-14T06:24:44,556 copying medspacy/postprocess/__init__.py -> build/lib/medspacy/postprocess 2023-05-14T06:24:44,557 copying medspacy/postprocess/postprocessing_rule.py -> build/lib/medspacy/postprocess 2023-05-14T06:24:44,559 copying medspacy/postprocess/postprocessing_pattern.py -> build/lib/medspacy/postprocess 2023-05-14T06:24:44,562 creating build/lib/medspacy/context 2023-05-14T06:24:44,563 copying medspacy/context/context_rule.py -> build/lib/medspacy/context 2023-05-14T06:24:44,565 copying medspacy/context/__init__.py -> build/lib/medspacy/context 2023-05-14T06:24:44,567 copying medspacy/context/util.py -> build/lib/medspacy/context 2023-05-14T06:24:44,568 copying medspacy/context/context.py -> build/lib/medspacy/context 2023-05-14T06:24:44,571 copying medspacy/context/context_modifier.py -> build/lib/medspacy/context 2023-05-14T06:24:44,573 copying medspacy/context/context_graph.py -> build/lib/medspacy/context 2023-05-14T06:24:44,576 creating build/lib/medspacy/io 2023-05-14T06:24:44,577 copying medspacy/io/pipeline.py -> build/lib/medspacy/io 2023-05-14T06:24:44,579 copying medspacy/io/db.py -> build/lib/medspacy/io 2023-05-14T06:24:44,581 copying medspacy/io/config_example.py -> build/lib/medspacy/io 2023-05-14T06:24:44,583 copying medspacy/io/__init__.py -> build/lib/medspacy/io 2023-05-14T06:24:44,585 copying medspacy/io/db_connect.py -> build/lib/medspacy/io 2023-05-14T06:24:44,586 copying medspacy/io/db_writer.py -> build/lib/medspacy/io 2023-05-14T06:24:44,589 copying medspacy/io/doc_consumer.py -> build/lib/medspacy/io 2023-05-14T06:24:44,591 copying medspacy/io/db_reader.py -> build/lib/medspacy/io 2023-05-14T06:24:44,593 creating build/lib/medspacy/target_matcher 2023-05-14T06:24:44,594 copying medspacy/target_matcher/target_matcher.py -> build/lib/medspacy/target_matcher 2023-05-14T06:24:44,597 copying medspacy/target_matcher/target_rule.py -> build/lib/medspacy/target_matcher 2023-05-14T06:24:44,599 copying medspacy/target_matcher/__init__.py -> build/lib/medspacy/target_matcher 2023-05-14T06:24:44,601 copying medspacy/target_matcher/concept_tagger.py -> build/lib/medspacy/target_matcher 2023-05-14T06:24:44,603 creating build/lib/medspacy/section_detection 2023-05-14T06:24:44,604 copying medspacy/section_detection/section_rule.py -> build/lib/medspacy/section_detection 2023-05-14T06:24:44,607 copying medspacy/section_detection/sectionizer.py -> build/lib/medspacy/section_detection 2023-05-14T06:24:44,609 copying medspacy/section_detection/__init__.py -> build/lib/medspacy/section_detection 2023-05-14T06:24:44,611 copying medspacy/section_detection/section.py -> build/lib/medspacy/section_detection 2023-05-14T06:24:44,613 copying medspacy/section_detection/util.py -> build/lib/medspacy/section_detection 2023-05-14T06:24:44,616 creating build/lib/medspacy/common 2023-05-14T06:24:44,617 copying medspacy/common/base_rule.py -> build/lib/medspacy/common 2023-05-14T06:24:44,618 copying medspacy/common/medspacy_matcher.py -> build/lib/medspacy/common 2023-05-14T06:24:44,621 copying medspacy/common/__init__.py -> build/lib/medspacy/common 2023-05-14T06:24:44,622 copying medspacy/common/util.py -> build/lib/medspacy/common 2023-05-14T06:24:44,624 copying medspacy/common/regex_matcher.py -> build/lib/medspacy/common 2023-05-14T06:24:44,627 creating build/lib/medspacy/preprocess 2023-05-14T06:24:44,628 copying medspacy/preprocess/__init__.py -> build/lib/medspacy/preprocess 2023-05-14T06:24:44,630 copying medspacy/preprocess/preprocessor.py -> build/lib/medspacy/preprocess 2023-05-14T06:24:44,632 copying medspacy/preprocess/preprocessing_rule.py -> build/lib/medspacy/preprocess 2023-05-14T06:24:44,634 running egg_info 2023-05-14T06:24:44,646 writing medspacy.egg-info/PKG-INFO 2023-05-14T06:24:44,648 writing dependency_links to medspacy.egg-info/dependency_links.txt 2023-05-14T06:24:44,650 writing requirements to medspacy.egg-info/requires.txt 2023-05-14T06:24:44,651 writing top-level names to medspacy.egg-info/top_level.txt 2023-05-14T06:24:44,696 listing git files failed - pretending there aren't any 2023-05-14T06:24:44,703 reading manifest file 'medspacy.egg-info/SOURCES.txt' 2023-05-14T06:24:44,708 adding license file 'LICENSE' 2023-05-14T06:24:44,718 writing manifest file 'medspacy.egg-info/SOURCES.txt' 2023-05-14T06:24:44,744 creating build/lib/resources 2023-05-14T06:24:44,745 copying medspacy/../resources/context_rules.json -> build/lib/medspacy/../resources 2023-05-14T06:24:44,749 copying medspacy/../resources/rush_rules.tsv -> build/lib/medspacy/../resources 2023-05-14T06:24:44,752 copying medspacy/../resources/section_patterns.json -> build/lib/medspacy/../resources 2023-05-14T06:24:44,755 creating build/lib/resources/quickumls 2023-05-14T06:24:44,755 creating build/lib/resources/quickumls/QuickUMLS_SAMPLE_lowercase_POSIX_unqlite 2023-05-14T06:24:44,757 copying medspacy/../resources/quickumls/QuickUMLS_SAMPLE_lowercase_POSIX_unqlite/README.md -> build/lib/medspacy/../resources/quickumls/QuickUMLS_SAMPLE_lowercase_POSIX_unqlite 2023-05-14T06:24:44,759 copying medspacy/../resources/quickumls/QuickUMLS_SAMPLE_lowercase_POSIX_unqlite/database_backend.flag -> build/lib/medspacy/../resources/quickumls/QuickUMLS_SAMPLE_lowercase_POSIX_unqlite 2023-05-14T06:24:44,761 copying medspacy/../resources/quickumls/QuickUMLS_SAMPLE_lowercase_POSIX_unqlite/language.flag -> build/lib/medspacy/../resources/quickumls/QuickUMLS_SAMPLE_lowercase_POSIX_unqlite 2023-05-14T06:24:44,763 copying medspacy/../resources/quickumls/QuickUMLS_SAMPLE_lowercase_POSIX_unqlite/lowercase.flag -> build/lib/medspacy/../resources/quickumls/QuickUMLS_SAMPLE_lowercase_POSIX_unqlite 2023-05-14T06:24:44,765 copying medspacy/../resources/quickumls/QuickUMLS_SAMPLE_lowercase_POSIX_unqlite/normalize-unicode.flag -> build/lib/medspacy/../resources/quickumls/QuickUMLS_SAMPLE_lowercase_POSIX_unqlite 2023-05-14T06:24:44,767 creating build/lib/resources/quickumls/QuickUMLS_SAMPLE_lowercase_POSIX_unqlite/cui-semtypes.db 2023-05-14T06:24:44,768 copying medspacy/../resources/quickumls/QuickUMLS_SAMPLE_lowercase_POSIX_unqlite/cui-semtypes.db/cui.unqlite -> build/lib/medspacy/../resources/quickumls/QuickUMLS_SAMPLE_lowercase_POSIX_unqlite/cui-semtypes.db 2023-05-14T06:24:44,771 copying medspacy/../resources/quickumls/QuickUMLS_SAMPLE_lowercase_POSIX_unqlite/cui-semtypes.db/semtypes.unqlite -> build/lib/medspacy/../resources/quickumls/QuickUMLS_SAMPLE_lowercase_POSIX_unqlite/cui-semtypes.db 2023-05-14T06:24:44,773 creating build/lib/resources/quickumls/QuickUMLS_SAMPLE_lowercase_POSIX_unqlite/umls-simstring.db 2023-05-14T06:24:44,774 copying medspacy/../resources/quickumls/QuickUMLS_SAMPLE_lowercase_POSIX_unqlite/umls-simstring.db/umls-terms.simstring -> build/lib/medspacy/../resources/quickumls/QuickUMLS_SAMPLE_lowercase_POSIX_unqlite/umls-simstring.db 2023-05-14T06:24:44,777 copying medspacy/../resources/quickumls/QuickUMLS_SAMPLE_lowercase_POSIX_unqlite/umls-simstring.db/umls-terms.simstring.120.cdb -> build/lib/medspacy/../resources/quickumls/QuickUMLS_SAMPLE_lowercase_POSIX_unqlite/umls-simstring.db 2023-05-14T06:24:44,779 copying medspacy/../resources/quickumls/QuickUMLS_SAMPLE_lowercase_POSIX_unqlite/umls-simstring.db/umls-terms.simstring.14.cdb -> build/lib/medspacy/../resources/quickumls/QuickUMLS_SAMPLE_lowercase_POSIX_unqlite/umls-simstring.db 2023-05-14T06:24:44,782 copying medspacy/../resources/quickumls/QuickUMLS_SAMPLE_lowercase_POSIX_unqlite/umls-simstring.db/umls-terms.simstring.15.cdb -> build/lib/medspacy/../resources/quickumls/QuickUMLS_SAMPLE_lowercase_POSIX_unqlite/umls-simstring.db 2023-05-14T06:24:44,784 copying medspacy/../resources/quickumls/QuickUMLS_SAMPLE_lowercase_POSIX_unqlite/umls-simstring.db/umls-terms.simstring.17.cdb -> build/lib/medspacy/../resources/quickumls/QuickUMLS_SAMPLE_lowercase_POSIX_unqlite/umls-simstring.db 2023-05-14T06:24:44,786 copying medspacy/../resources/quickumls/QuickUMLS_SAMPLE_lowercase_POSIX_unqlite/umls-simstring.db/umls-terms.simstring.20.cdb -> build/lib/medspacy/../resources/quickumls/QuickUMLS_SAMPLE_lowercase_POSIX_unqlite/umls-simstring.db 2023-05-14T06:24:44,789 copying medspacy/../resources/quickumls/QuickUMLS_SAMPLE_lowercase_POSIX_unqlite/umls-simstring.db/umls-terms.simstring.21.cdb -> build/lib/medspacy/../resources/quickumls/QuickUMLS_SAMPLE_lowercase_POSIX_unqlite/umls-simstring.db 2023-05-14T06:24:44,791 copying medspacy/../resources/quickumls/QuickUMLS_SAMPLE_lowercase_POSIX_unqlite/umls-simstring.db/umls-terms.simstring.22.cdb -> build/lib/medspacy/../resources/quickumls/QuickUMLS_SAMPLE_lowercase_POSIX_unqlite/umls-simstring.db 2023-05-14T06:24:44,793 copying medspacy/../resources/quickumls/QuickUMLS_SAMPLE_lowercase_POSIX_unqlite/umls-simstring.db/umls-terms.simstring.24.cdb -> build/lib/medspacy/../resources/quickumls/QuickUMLS_SAMPLE_lowercase_POSIX_unqlite/umls-simstring.db 2023-05-14T06:24:44,795 copying medspacy/../resources/quickumls/QuickUMLS_SAMPLE_lowercase_POSIX_unqlite/umls-simstring.db/umls-terms.simstring.26.cdb -> build/lib/medspacy/../resources/quickumls/QuickUMLS_SAMPLE_lowercase_POSIX_unqlite/umls-simstring.db 2023-05-14T06:24:44,797 copying medspacy/../resources/quickumls/QuickUMLS_SAMPLE_lowercase_POSIX_unqlite/umls-simstring.db/umls-terms.simstring.27.cdb -> build/lib/medspacy/../resources/quickumls/QuickUMLS_SAMPLE_lowercase_POSIX_unqlite/umls-simstring.db 2023-05-14T06:24:44,800 copying medspacy/../resources/quickumls/QuickUMLS_SAMPLE_lowercase_POSIX_unqlite/umls-simstring.db/umls-terms.simstring.28.cdb -> build/lib/medspacy/../resources/quickumls/QuickUMLS_SAMPLE_lowercase_POSIX_unqlite/umls-simstring.db 2023-05-14T06:24:44,803 copying medspacy/../resources/quickumls/QuickUMLS_SAMPLE_lowercase_POSIX_unqlite/umls-simstring.db/umls-terms.simstring.29.cdb -> build/lib/medspacy/../resources/quickumls/QuickUMLS_SAMPLE_lowercase_POSIX_unqlite/umls-simstring.db 2023-05-14T06:24:44,805 copying medspacy/../resources/quickumls/QuickUMLS_SAMPLE_lowercase_POSIX_unqlite/umls-simstring.db/umls-terms.simstring.30.cdb -> build/lib/medspacy/../resources/quickumls/QuickUMLS_SAMPLE_lowercase_POSIX_unqlite/umls-simstring.db 2023-05-14T06:24:44,807 copying medspacy/../resources/quickumls/QuickUMLS_SAMPLE_lowercase_POSIX_unqlite/umls-simstring.db/umls-terms.simstring.31.cdb -> build/lib/medspacy/../resources/quickumls/QuickUMLS_SAMPLE_lowercase_POSIX_unqlite/umls-simstring.db 2023-05-14T06:24:44,810 copying medspacy/../resources/quickumls/QuickUMLS_SAMPLE_lowercase_POSIX_unqlite/umls-simstring.db/umls-terms.simstring.32.cdb -> build/lib/medspacy/../resources/quickumls/QuickUMLS_SAMPLE_lowercase_POSIX_unqlite/umls-simstring.db 2023-05-14T06:24:44,812 copying medspacy/../resources/quickumls/QuickUMLS_SAMPLE_lowercase_POSIX_unqlite/umls-simstring.db/umls-terms.simstring.33.cdb -> build/lib/medspacy/../resources/quickumls/QuickUMLS_SAMPLE_lowercase_POSIX_unqlite/umls-simstring.db 2023-05-14T06:24:44,815 copying medspacy/../resources/quickumls/QuickUMLS_SAMPLE_lowercase_POSIX_unqlite/umls-simstring.db/umls-terms.simstring.35.cdb -> build/lib/medspacy/../resources/quickumls/QuickUMLS_SAMPLE_lowercase_POSIX_unqlite/umls-simstring.db 2023-05-14T06:24:44,817 copying medspacy/../resources/quickumls/QuickUMLS_SAMPLE_lowercase_POSIX_unqlite/umls-simstring.db/umls-terms.simstring.37.cdb -> build/lib/medspacy/../resources/quickumls/QuickUMLS_SAMPLE_lowercase_POSIX_unqlite/umls-simstring.db 2023-05-14T06:24:44,819 copying medspacy/../resources/quickumls/QuickUMLS_SAMPLE_lowercase_POSIX_unqlite/umls-simstring.db/umls-terms.simstring.38.cdb -> build/lib/medspacy/../resources/quickumls/QuickUMLS_SAMPLE_lowercase_POSIX_unqlite/umls-simstring.db 2023-05-14T06:24:44,821 copying medspacy/../resources/quickumls/QuickUMLS_SAMPLE_lowercase_POSIX_unqlite/umls-simstring.db/umls-terms.simstring.39.cdb -> build/lib/medspacy/../resources/quickumls/QuickUMLS_SAMPLE_lowercase_POSIX_unqlite/umls-simstring.db 2023-05-14T06:24:44,823 copying medspacy/../resources/quickumls/QuickUMLS_SAMPLE_lowercase_POSIX_unqlite/umls-simstring.db/umls-terms.simstring.40.cdb -> build/lib/medspacy/../resources/quickumls/QuickUMLS_SAMPLE_lowercase_POSIX_unqlite/umls-simstring.db 2023-05-14T06:24:44,826 copying medspacy/../resources/quickumls/QuickUMLS_SAMPLE_lowercase_POSIX_unqlite/umls-simstring.db/umls-terms.simstring.43.cdb -> build/lib/medspacy/../resources/quickumls/QuickUMLS_SAMPLE_lowercase_POSIX_unqlite/umls-simstring.db 2023-05-14T06:24:44,828 copying medspacy/../resources/quickumls/QuickUMLS_SAMPLE_lowercase_POSIX_unqlite/umls-simstring.db/umls-terms.simstring.79.cdb -> build/lib/medspacy/../resources/quickumls/QuickUMLS_SAMPLE_lowercase_POSIX_unqlite/umls-simstring.db 2023-05-14T06:24:44,831 copying medspacy/../resources/quickumls/QuickUMLS_SAMPLE_lowercase_POSIX_unqlite/umls-simstring.db/umls-terms.simstring.8.cdb -> build/lib/medspacy/../resources/quickumls/QuickUMLS_SAMPLE_lowercase_POSIX_unqlite/umls-simstring.db 2023-05-14T06:24:44,833 creating build/lib/resources/quickumls/QuickUMLS_SAMPLE_lowercase_Windows_unqlite 2023-05-14T06:24:44,834 copying medspacy/../resources/quickumls/QuickUMLS_SAMPLE_lowercase_Windows_unqlite/README.md -> build/lib/medspacy/../resources/quickumls/QuickUMLS_SAMPLE_lowercase_Windows_unqlite 2023-05-14T06:24:44,836 copying medspacy/../resources/quickumls/QuickUMLS_SAMPLE_lowercase_Windows_unqlite/database_backend.flag -> build/lib/medspacy/../resources/quickumls/QuickUMLS_SAMPLE_lowercase_Windows_unqlite 2023-05-14T06:24:44,838 copying medspacy/../resources/quickumls/QuickUMLS_SAMPLE_lowercase_Windows_unqlite/language.flag -> build/lib/medspacy/../resources/quickumls/QuickUMLS_SAMPLE_lowercase_Windows_unqlite 2023-05-14T06:24:44,840 copying medspacy/../resources/quickumls/QuickUMLS_SAMPLE_lowercase_Windows_unqlite/lowercase.flag -> build/lib/medspacy/../resources/quickumls/QuickUMLS_SAMPLE_lowercase_Windows_unqlite 2023-05-14T06:24:44,842 copying medspacy/../resources/quickumls/QuickUMLS_SAMPLE_lowercase_Windows_unqlite/normalize-unicode.flag -> build/lib/medspacy/../resources/quickumls/QuickUMLS_SAMPLE_lowercase_Windows_unqlite 2023-05-14T06:24:44,844 creating build/lib/resources/quickumls/QuickUMLS_SAMPLE_lowercase_Windows_unqlite/cui-semtypes.db 2023-05-14T06:24:44,845 copying medspacy/../resources/quickumls/QuickUMLS_SAMPLE_lowercase_Windows_unqlite/cui-semtypes.db/cui.unqlite -> build/lib/medspacy/../resources/quickumls/QuickUMLS_SAMPLE_lowercase_Windows_unqlite/cui-semtypes.db 2023-05-14T06:24:44,848 copying medspacy/../resources/quickumls/QuickUMLS_SAMPLE_lowercase_Windows_unqlite/cui-semtypes.db/semtypes.unqlite -> build/lib/medspacy/../resources/quickumls/QuickUMLS_SAMPLE_lowercase_Windows_unqlite/cui-semtypes.db 2023-05-14T06:24:44,850 creating build/lib/resources/quickumls/QuickUMLS_SAMPLE_lowercase_Windows_unqlite/umls-simstring.db 2023-05-14T06:24:44,851 copying medspacy/../resources/quickumls/QuickUMLS_SAMPLE_lowercase_Windows_unqlite/umls-simstring.db/umls-terms.simstring -> build/lib/medspacy/../resources/quickumls/QuickUMLS_SAMPLE_lowercase_Windows_unqlite/umls-simstring.db 2023-05-14T06:24:44,854 copying medspacy/../resources/quickumls/QuickUMLS_SAMPLE_lowercase_Windows_unqlite/umls-simstring.db/umls-terms.simstring.120.cdb -> build/lib/medspacy/../resources/quickumls/QuickUMLS_SAMPLE_lowercase_Windows_unqlite/umls-simstring.db 2023-05-14T06:24:44,856 copying medspacy/../resources/quickumls/QuickUMLS_SAMPLE_lowercase_Windows_unqlite/umls-simstring.db/umls-terms.simstring.14.cdb -> build/lib/medspacy/../resources/quickumls/QuickUMLS_SAMPLE_lowercase_Windows_unqlite/umls-simstring.db 2023-05-14T06:24:44,859 copying medspacy/../resources/quickumls/QuickUMLS_SAMPLE_lowercase_Windows_unqlite/umls-simstring.db/umls-terms.simstring.15.cdb -> build/lib/medspacy/../resources/quickumls/QuickUMLS_SAMPLE_lowercase_Windows_unqlite/umls-simstring.db 2023-05-14T06:24:44,861 copying medspacy/../resources/quickumls/QuickUMLS_SAMPLE_lowercase_Windows_unqlite/umls-simstring.db/umls-terms.simstring.17.cdb -> build/lib/medspacy/../resources/quickumls/QuickUMLS_SAMPLE_lowercase_Windows_unqlite/umls-simstring.db 2023-05-14T06:24:44,863 copying medspacy/../resources/quickumls/QuickUMLS_SAMPLE_lowercase_Windows_unqlite/umls-simstring.db/umls-terms.simstring.20.cdb -> build/lib/medspacy/../resources/quickumls/QuickUMLS_SAMPLE_lowercase_Windows_unqlite/umls-simstring.db 2023-05-14T06:24:44,865 copying medspacy/../resources/quickumls/QuickUMLS_SAMPLE_lowercase_Windows_unqlite/umls-simstring.db/umls-terms.simstring.21.cdb -> build/lib/medspacy/../resources/quickumls/QuickUMLS_SAMPLE_lowercase_Windows_unqlite/umls-simstring.db 2023-05-14T06:24:44,867 copying medspacy/../resources/quickumls/QuickUMLS_SAMPLE_lowercase_Windows_unqlite/umls-simstring.db/umls-terms.simstring.22.cdb -> build/lib/medspacy/../resources/quickumls/QuickUMLS_SAMPLE_lowercase_Windows_unqlite/umls-simstring.db 2023-05-14T06:24:44,870 copying medspacy/../resources/quickumls/QuickUMLS_SAMPLE_lowercase_Windows_unqlite/umls-simstring.db/umls-terms.simstring.24.cdb -> build/lib/medspacy/../resources/quickumls/QuickUMLS_SAMPLE_lowercase_Windows_unqlite/umls-simstring.db 2023-05-14T06:24:44,872 copying medspacy/../resources/quickumls/QuickUMLS_SAMPLE_lowercase_Windows_unqlite/umls-simstring.db/umls-terms.simstring.26.cdb -> build/lib/medspacy/../resources/quickumls/QuickUMLS_SAMPLE_lowercase_Windows_unqlite/umls-simstring.db 2023-05-14T06:24:44,874 copying medspacy/../resources/quickumls/QuickUMLS_SAMPLE_lowercase_Windows_unqlite/umls-simstring.db/umls-terms.simstring.27.cdb -> build/lib/medspacy/../resources/quickumls/QuickUMLS_SAMPLE_lowercase_Windows_unqlite/umls-simstring.db 2023-05-14T06:24:44,877 copying medspacy/../resources/quickumls/QuickUMLS_SAMPLE_lowercase_Windows_unqlite/umls-simstring.db/umls-terms.simstring.28.cdb -> build/lib/medspacy/../resources/quickumls/QuickUMLS_SAMPLE_lowercase_Windows_unqlite/umls-simstring.db 2023-05-14T06:24:44,879 copying medspacy/../resources/quickumls/QuickUMLS_SAMPLE_lowercase_Windows_unqlite/umls-simstring.db/umls-terms.simstring.29.cdb -> build/lib/medspacy/../resources/quickumls/QuickUMLS_SAMPLE_lowercase_Windows_unqlite/umls-simstring.db 2023-05-14T06:24:44,881 copying medspacy/../resources/quickumls/QuickUMLS_SAMPLE_lowercase_Windows_unqlite/umls-simstring.db/umls-terms.simstring.30.cdb -> build/lib/medspacy/../resources/quickumls/QuickUMLS_SAMPLE_lowercase_Windows_unqlite/umls-simstring.db 2023-05-14T06:24:44,884 copying medspacy/../resources/quickumls/QuickUMLS_SAMPLE_lowercase_Windows_unqlite/umls-simstring.db/umls-terms.simstring.31.cdb -> build/lib/medspacy/../resources/quickumls/QuickUMLS_SAMPLE_lowercase_Windows_unqlite/umls-simstring.db 2023-05-14T06:24:44,886 copying medspacy/../resources/quickumls/QuickUMLS_SAMPLE_lowercase_Windows_unqlite/umls-simstring.db/umls-terms.simstring.32.cdb -> build/lib/medspacy/../resources/quickumls/QuickUMLS_SAMPLE_lowercase_Windows_unqlite/umls-simstring.db 2023-05-14T06:24:44,888 copying medspacy/../resources/quickumls/QuickUMLS_SAMPLE_lowercase_Windows_unqlite/umls-simstring.db/umls-terms.simstring.33.cdb -> build/lib/medspacy/../resources/quickumls/QuickUMLS_SAMPLE_lowercase_Windows_unqlite/umls-simstring.db 2023-05-14T06:24:44,891 copying medspacy/../resources/quickumls/QuickUMLS_SAMPLE_lowercase_Windows_unqlite/umls-simstring.db/umls-terms.simstring.35.cdb -> build/lib/medspacy/../resources/quickumls/QuickUMLS_SAMPLE_lowercase_Windows_unqlite/umls-simstring.db 2023-05-14T06:24:44,893 copying medspacy/../resources/quickumls/QuickUMLS_SAMPLE_lowercase_Windows_unqlite/umls-simstring.db/umls-terms.simstring.37.cdb -> build/lib/medspacy/../resources/quickumls/QuickUMLS_SAMPLE_lowercase_Windows_unqlite/umls-simstring.db 2023-05-14T06:24:44,895 copying medspacy/../resources/quickumls/QuickUMLS_SAMPLE_lowercase_Windows_unqlite/umls-simstring.db/umls-terms.simstring.38.cdb -> build/lib/medspacy/../resources/quickumls/QuickUMLS_SAMPLE_lowercase_Windows_unqlite/umls-simstring.db 2023-05-14T06:24:44,898 copying medspacy/../resources/quickumls/QuickUMLS_SAMPLE_lowercase_Windows_unqlite/umls-simstring.db/umls-terms.simstring.39.cdb -> build/lib/medspacy/../resources/quickumls/QuickUMLS_SAMPLE_lowercase_Windows_unqlite/umls-simstring.db 2023-05-14T06:24:44,900 copying medspacy/../resources/quickumls/QuickUMLS_SAMPLE_lowercase_Windows_unqlite/umls-simstring.db/umls-terms.simstring.40.cdb -> build/lib/medspacy/../resources/quickumls/QuickUMLS_SAMPLE_lowercase_Windows_unqlite/umls-simstring.db 2023-05-14T06:24:44,903 copying medspacy/../resources/quickumls/QuickUMLS_SAMPLE_lowercase_Windows_unqlite/umls-simstring.db/umls-terms.simstring.43.cdb -> build/lib/medspacy/../resources/quickumls/QuickUMLS_SAMPLE_lowercase_Windows_unqlite/umls-simstring.db 2023-05-14T06:24:44,905 copying medspacy/../resources/quickumls/QuickUMLS_SAMPLE_lowercase_Windows_unqlite/umls-simstring.db/umls-terms.simstring.79.cdb -> build/lib/medspacy/../resources/quickumls/QuickUMLS_SAMPLE_lowercase_Windows_unqlite/umls-simstring.db 2023-05-14T06:24:44,907 copying medspacy/../resources/quickumls/QuickUMLS_SAMPLE_lowercase_Windows_unqlite/umls-simstring.db/umls-terms.simstring.8.cdb -> build/lib/medspacy/../resources/quickumls/QuickUMLS_SAMPLE_lowercase_Windows_unqlite/umls-simstring.db 2023-05-14T06:24:44,954 installing to build/bdist.linux-aarch64/wheel 2023-05-14T06:24:44,954 running install 2023-05-14T06:24:44,980 running install_lib 2023-05-14T06:24:44,986 creating build/bdist.linux-aarch64 2023-05-14T06:24:44,987 creating build/bdist.linux-aarch64/wheel 2023-05-14T06:24:44,989 creating build/bdist.linux-aarch64/wheel/medspacy 2023-05-14T06:24:44,990 copying build/lib/medspacy/ner.py -> build/bdist.linux-aarch64/wheel/medspacy 2023-05-14T06:24:44,992 creating build/bdist.linux-aarch64/wheel/medspacy/postprocess 2023-05-14T06:24:44,993 copying build/lib/medspacy/postprocess/postprocessor.py -> build/bdist.linux-aarch64/wheel/medspacy/postprocess 2023-05-14T06:24:44,995 copying build/lib/medspacy/postprocess/postprocessing_functions.py -> build/bdist.linux-aarch64/wheel/medspacy/postprocess 2023-05-14T06:24:44,998 copying build/lib/medspacy/postprocess/__init__.py -> build/bdist.linux-aarch64/wheel/medspacy/postprocess 2023-05-14T06:24:45,000 copying build/lib/medspacy/postprocess/postprocessing_rule.py -> build/bdist.linux-aarch64/wheel/medspacy/postprocess 2023-05-14T06:24:45,002 copying build/lib/medspacy/postprocess/postprocessing_pattern.py -> build/bdist.linux-aarch64/wheel/medspacy/postprocess 2023-05-14T06:24:45,004 creating build/bdist.linux-aarch64/wheel/medspacy/context 2023-05-14T06:24:45,005 copying build/lib/medspacy/context/context_rule.py -> build/bdist.linux-aarch64/wheel/medspacy/context 2023-05-14T06:24:45,008 copying build/lib/medspacy/context/__init__.py -> build/bdist.linux-aarch64/wheel/medspacy/context 2023-05-14T06:24:45,010 copying build/lib/medspacy/context/util.py -> build/bdist.linux-aarch64/wheel/medspacy/context 2023-05-14T06:24:45,011 copying build/lib/medspacy/context/context.py -> build/bdist.linux-aarch64/wheel/medspacy/context 2023-05-14T06:24:45,014 copying build/lib/medspacy/context/context_modifier.py -> build/bdist.linux-aarch64/wheel/medspacy/context 2023-05-14T06:24:45,017 copying build/lib/medspacy/context/context_graph.py -> build/bdist.linux-aarch64/wheel/medspacy/context 2023-05-14T06:24:45,019 copying build/lib/medspacy/_version.py -> build/bdist.linux-aarch64/wheel/medspacy 2023-05-14T06:24:45,021 copying build/lib/medspacy/visualization.py -> build/bdist.linux-aarch64/wheel/medspacy 2023-05-14T06:24:45,023 copying build/lib/medspacy/sentence_splitting.py -> build/bdist.linux-aarch64/wheel/medspacy 2023-05-14T06:24:45,025 copying build/lib/medspacy/__init__.py -> build/bdist.linux-aarch64/wheel/medspacy 2023-05-14T06:24:45,027 copying build/lib/medspacy/util.py -> build/bdist.linux-aarch64/wheel/medspacy 2023-05-14T06:24:45,029 copying build/lib/medspacy/components.py -> build/bdist.linux-aarch64/wheel/medspacy 2023-05-14T06:24:45,031 copying build/lib/medspacy/custom_tokenizer.py -> build/bdist.linux-aarch64/wheel/medspacy 2023-05-14T06:24:45,033 creating build/bdist.linux-aarch64/wheel/medspacy/io 2023-05-14T06:24:45,034 copying build/lib/medspacy/io/pipeline.py -> build/bdist.linux-aarch64/wheel/medspacy/io 2023-05-14T06:24:45,036 copying build/lib/medspacy/io/db.py -> build/bdist.linux-aarch64/wheel/medspacy/io 2023-05-14T06:24:45,038 copying build/lib/medspacy/io/config_example.py -> build/bdist.linux-aarch64/wheel/medspacy/io 2023-05-14T06:24:45,040 copying build/lib/medspacy/io/__init__.py -> build/bdist.linux-aarch64/wheel/medspacy/io 2023-05-14T06:24:45,042 copying build/lib/medspacy/io/db_connect.py -> build/bdist.linux-aarch64/wheel/medspacy/io 2023-05-14T06:24:45,044 copying build/lib/medspacy/io/db_writer.py -> build/bdist.linux-aarch64/wheel/medspacy/io 2023-05-14T06:24:45,046 copying build/lib/medspacy/io/doc_consumer.py -> build/bdist.linux-aarch64/wheel/medspacy/io 2023-05-14T06:24:45,048 copying build/lib/medspacy/io/db_reader.py -> build/bdist.linux-aarch64/wheel/medspacy/io 2023-05-14T06:24:45,051 creating build/bdist.linux-aarch64/wheel/medspacy/target_matcher 2023-05-14T06:24:45,052 copying build/lib/medspacy/target_matcher/target_matcher.py -> build/bdist.linux-aarch64/wheel/medspacy/target_matcher 2023-05-14T06:24:45,054 copying build/lib/medspacy/target_matcher/target_rule.py -> build/bdist.linux-aarch64/wheel/medspacy/target_matcher 2023-05-14T06:24:45,057 copying build/lib/medspacy/target_matcher/__init__.py -> build/bdist.linux-aarch64/wheel/medspacy/target_matcher 2023-05-14T06:24:45,058 copying build/lib/medspacy/target_matcher/concept_tagger.py -> build/bdist.linux-aarch64/wheel/medspacy/target_matcher 2023-05-14T06:24:45,061 creating build/bdist.linux-aarch64/wheel/medspacy/section_detection 2023-05-14T06:24:45,062 copying build/lib/medspacy/section_detection/section_rule.py -> build/bdist.linux-aarch64/wheel/medspacy/section_detection 2023-05-14T06:24:45,064 copying build/lib/medspacy/section_detection/sectionizer.py -> build/bdist.linux-aarch64/wheel/medspacy/section_detection 2023-05-14T06:24:45,067 copying build/lib/medspacy/section_detection/__init__.py -> build/bdist.linux-aarch64/wheel/medspacy/section_detection 2023-05-14T06:24:45,069 copying build/lib/medspacy/section_detection/section.py -> build/bdist.linux-aarch64/wheel/medspacy/section_detection 2023-05-14T06:24:45,071 copying build/lib/medspacy/section_detection/util.py -> build/bdist.linux-aarch64/wheel/medspacy/section_detection 2023-05-14T06:24:45,073 creating build/bdist.linux-aarch64/wheel/medspacy/common 2023-05-14T06:24:45,074 copying build/lib/medspacy/common/base_rule.py -> build/bdist.linux-aarch64/wheel/medspacy/common 2023-05-14T06:24:45,076 copying build/lib/medspacy/common/medspacy_matcher.py -> build/bdist.linux-aarch64/wheel/medspacy/common 2023-05-14T06:24:45,079 copying build/lib/medspacy/common/__init__.py -> build/bdist.linux-aarch64/wheel/medspacy/common 2023-05-14T06:24:45,081 copying build/lib/medspacy/common/util.py -> build/bdist.linux-aarch64/wheel/medspacy/common 2023-05-14T06:24:45,083 copying build/lib/medspacy/common/regex_matcher.py -> build/bdist.linux-aarch64/wheel/medspacy/common 2023-05-14T06:24:45,085 copying build/lib/medspacy/_extensions.py -> build/bdist.linux-aarch64/wheel/medspacy 2023-05-14T06:24:45,088 creating build/bdist.linux-aarch64/wheel/medspacy/preprocess 2023-05-14T06:24:45,089 copying build/lib/medspacy/preprocess/__init__.py -> build/bdist.linux-aarch64/wheel/medspacy/preprocess 2023-05-14T06:24:45,091 copying build/lib/medspacy/preprocess/preprocessor.py -> build/bdist.linux-aarch64/wheel/medspacy/preprocess 2023-05-14T06:24:45,093 copying build/lib/medspacy/preprocess/preprocessing_rule.py -> build/bdist.linux-aarch64/wheel/medspacy/preprocess 2023-05-14T06:24:45,096 creating build/bdist.linux-aarch64/wheel/resources 2023-05-14T06:24:45,097 copying build/lib/resources/context_rules.json -> build/bdist.linux-aarch64/wheel/resources 2023-05-14T06:24:45,101 copying build/lib/resources/rush_rules.tsv -> build/bdist.linux-aarch64/wheel/resources 2023-05-14T06:24:45,105 creating build/bdist.linux-aarch64/wheel/resources/quickumls 2023-05-14T06:24:45,106 creating build/bdist.linux-aarch64/wheel/resources/quickumls/QuickUMLS_SAMPLE_lowercase_Windows_unqlite 2023-05-14T06:24:45,108 creating build/bdist.linux-aarch64/wheel/resources/quickumls/QuickUMLS_SAMPLE_lowercase_Windows_unqlite/cui-semtypes.db 2023-05-14T06:24:45,109 copying build/lib/resources/quickumls/QuickUMLS_SAMPLE_lowercase_Windows_unqlite/cui-semtypes.db/semtypes.unqlite -> build/bdist.linux-aarch64/wheel/resources/quickumls/QuickUMLS_SAMPLE_lowercase_Windows_unqlite/cui-semtypes.db 2023-05-14T06:24:45,111 copying build/lib/resources/quickumls/QuickUMLS_SAMPLE_lowercase_Windows_unqlite/cui-semtypes.db/cui.unqlite -> build/bdist.linux-aarch64/wheel/resources/quickumls/QuickUMLS_SAMPLE_lowercase_Windows_unqlite/cui-semtypes.db 2023-05-14T06:24:45,114 copying build/lib/resources/quickumls/QuickUMLS_SAMPLE_lowercase_Windows_unqlite/database_backend.flag -> build/bdist.linux-aarch64/wheel/resources/quickumls/QuickUMLS_SAMPLE_lowercase_Windows_unqlite 2023-05-14T06:24:45,116 copying build/lib/resources/quickumls/QuickUMLS_SAMPLE_lowercase_Windows_unqlite/normalize-unicode.flag -> build/bdist.linux-aarch64/wheel/resources/quickumls/QuickUMLS_SAMPLE_lowercase_Windows_unqlite 2023-05-14T06:24:45,117 copying build/lib/resources/quickumls/QuickUMLS_SAMPLE_lowercase_Windows_unqlite/lowercase.flag -> build/bdist.linux-aarch64/wheel/resources/quickumls/QuickUMLS_SAMPLE_lowercase_Windows_unqlite 2023-05-14T06:24:45,120 creating build/bdist.linux-aarch64/wheel/resources/quickumls/QuickUMLS_SAMPLE_lowercase_Windows_unqlite/umls-simstring.db 2023-05-14T06:24:45,121 copying build/lib/resources/quickumls/QuickUMLS_SAMPLE_lowercase_Windows_unqlite/umls-simstring.db/umls-terms.simstring.35.cdb -> build/bdist.linux-aarch64/wheel/resources/quickumls/QuickUMLS_SAMPLE_lowercase_Windows_unqlite/umls-simstring.db 2023-05-14T06:24:45,123 copying build/lib/resources/quickumls/QuickUMLS_SAMPLE_lowercase_Windows_unqlite/umls-simstring.db/umls-terms.simstring.37.cdb -> build/bdist.linux-aarch64/wheel/resources/quickumls/QuickUMLS_SAMPLE_lowercase_Windows_unqlite/umls-simstring.db 2023-05-14T06:24:45,125 copying build/lib/resources/quickumls/QuickUMLS_SAMPLE_lowercase_Windows_unqlite/umls-simstring.db/umls-terms.simstring.38.cdb -> build/bdist.linux-aarch64/wheel/resources/quickumls/QuickUMLS_SAMPLE_lowercase_Windows_unqlite/umls-simstring.db 2023-05-14T06:24:45,127 copying build/lib/resources/quickumls/QuickUMLS_SAMPLE_lowercase_Windows_unqlite/umls-simstring.db/umls-terms.simstring.39.cdb -> build/bdist.linux-aarch64/wheel/resources/quickumls/QuickUMLS_SAMPLE_lowercase_Windows_unqlite/umls-simstring.db 2023-05-14T06:24:45,129 copying build/lib/resources/quickumls/QuickUMLS_SAMPLE_lowercase_Windows_unqlite/umls-simstring.db/umls-terms.simstring.27.cdb -> build/bdist.linux-aarch64/wheel/resources/quickumls/QuickUMLS_SAMPLE_lowercase_Windows_unqlite/umls-simstring.db 2023-05-14T06:24:45,131 copying build/lib/resources/quickumls/QuickUMLS_SAMPLE_lowercase_Windows_unqlite/umls-simstring.db/umls-terms.simstring.14.cdb -> build/bdist.linux-aarch64/wheel/resources/quickumls/QuickUMLS_SAMPLE_lowercase_Windows_unqlite/umls-simstring.db 2023-05-14T06:24:45,133 copying build/lib/resources/quickumls/QuickUMLS_SAMPLE_lowercase_Windows_unqlite/umls-simstring.db/umls-terms.simstring.79.cdb -> build/bdist.linux-aarch64/wheel/resources/quickumls/QuickUMLS_SAMPLE_lowercase_Windows_unqlite/umls-simstring.db 2023-05-14T06:24:45,136 copying build/lib/resources/quickumls/QuickUMLS_SAMPLE_lowercase_Windows_unqlite/umls-simstring.db/umls-terms.simstring.8.cdb -> build/bdist.linux-aarch64/wheel/resources/quickumls/QuickUMLS_SAMPLE_lowercase_Windows_unqlite/umls-simstring.db 2023-05-14T06:24:45,138 copying build/lib/resources/quickumls/QuickUMLS_SAMPLE_lowercase_Windows_unqlite/umls-simstring.db/umls-terms.simstring.24.cdb -> build/bdist.linux-aarch64/wheel/resources/quickumls/QuickUMLS_SAMPLE_lowercase_Windows_unqlite/umls-simstring.db 2023-05-14T06:24:45,140 copying build/lib/resources/quickumls/QuickUMLS_SAMPLE_lowercase_Windows_unqlite/umls-simstring.db/umls-terms.simstring.43.cdb -> build/bdist.linux-aarch64/wheel/resources/quickumls/QuickUMLS_SAMPLE_lowercase_Windows_unqlite/umls-simstring.db 2023-05-14T06:24:45,142 copying build/lib/resources/quickumls/QuickUMLS_SAMPLE_lowercase_Windows_unqlite/umls-simstring.db/umls-terms.simstring.20.cdb -> build/bdist.linux-aarch64/wheel/resources/quickumls/QuickUMLS_SAMPLE_lowercase_Windows_unqlite/umls-simstring.db 2023-05-14T06:24:45,144 copying build/lib/resources/quickumls/QuickUMLS_SAMPLE_lowercase_Windows_unqlite/umls-simstring.db/umls-terms.simstring.120.cdb -> build/bdist.linux-aarch64/wheel/resources/quickumls/QuickUMLS_SAMPLE_lowercase_Windows_unqlite/umls-simstring.db 2023-05-14T06:24:45,146 copying build/lib/resources/quickumls/QuickUMLS_SAMPLE_lowercase_Windows_unqlite/umls-simstring.db/umls-terms.simstring.15.cdb -> build/bdist.linux-aarch64/wheel/resources/quickumls/QuickUMLS_SAMPLE_lowercase_Windows_unqlite/umls-simstring.db 2023-05-14T06:24:45,148 copying build/lib/resources/quickumls/QuickUMLS_SAMPLE_lowercase_Windows_unqlite/umls-simstring.db/umls-terms.simstring.28.cdb -> build/bdist.linux-aarch64/wheel/resources/quickumls/QuickUMLS_SAMPLE_lowercase_Windows_unqlite/umls-simstring.db 2023-05-14T06:24:45,151 copying build/lib/resources/quickumls/QuickUMLS_SAMPLE_lowercase_Windows_unqlite/umls-simstring.db/umls-terms.simstring.21.cdb -> build/bdist.linux-aarch64/wheel/resources/quickumls/QuickUMLS_SAMPLE_lowercase_Windows_unqlite/umls-simstring.db 2023-05-14T06:24:45,153 copying build/lib/resources/quickumls/QuickUMLS_SAMPLE_lowercase_Windows_unqlite/umls-simstring.db/umls-terms.simstring -> build/bdist.linux-aarch64/wheel/resources/quickumls/QuickUMLS_SAMPLE_lowercase_Windows_unqlite/umls-simstring.db 2023-05-14T06:24:45,155 copying build/lib/resources/quickumls/QuickUMLS_SAMPLE_lowercase_Windows_unqlite/umls-simstring.db/umls-terms.simstring.22.cdb -> build/bdist.linux-aarch64/wheel/resources/quickumls/QuickUMLS_SAMPLE_lowercase_Windows_unqlite/umls-simstring.db 2023-05-14T06:24:45,157 copying build/lib/resources/quickumls/QuickUMLS_SAMPLE_lowercase_Windows_unqlite/umls-simstring.db/umls-terms.simstring.30.cdb -> build/bdist.linux-aarch64/wheel/resources/quickumls/QuickUMLS_SAMPLE_lowercase_Windows_unqlite/umls-simstring.db 2023-05-14T06:24:45,159 copying build/lib/resources/quickumls/QuickUMLS_SAMPLE_lowercase_Windows_unqlite/umls-simstring.db/umls-terms.simstring.29.cdb -> build/bdist.linux-aarch64/wheel/resources/quickumls/QuickUMLS_SAMPLE_lowercase_Windows_unqlite/umls-simstring.db 2023-05-14T06:24:45,161 copying build/lib/resources/quickumls/QuickUMLS_SAMPLE_lowercase_Windows_unqlite/umls-simstring.db/umls-terms.simstring.31.cdb -> build/bdist.linux-aarch64/wheel/resources/quickumls/QuickUMLS_SAMPLE_lowercase_Windows_unqlite/umls-simstring.db 2023-05-14T06:24:45,163 copying build/lib/resources/quickumls/QuickUMLS_SAMPLE_lowercase_Windows_unqlite/umls-simstring.db/umls-terms.simstring.26.cdb -> build/bdist.linux-aarch64/wheel/resources/quickumls/QuickUMLS_SAMPLE_lowercase_Windows_unqlite/umls-simstring.db 2023-05-14T06:24:45,165 copying build/lib/resources/quickumls/QuickUMLS_SAMPLE_lowercase_Windows_unqlite/umls-simstring.db/umls-terms.simstring.17.cdb -> build/bdist.linux-aarch64/wheel/resources/quickumls/QuickUMLS_SAMPLE_lowercase_Windows_unqlite/umls-simstring.db 2023-05-14T06:24:45,167 copying build/lib/resources/quickumls/QuickUMLS_SAMPLE_lowercase_Windows_unqlite/umls-simstring.db/umls-terms.simstring.32.cdb -> build/bdist.linux-aarch64/wheel/resources/quickumls/QuickUMLS_SAMPLE_lowercase_Windows_unqlite/umls-simstring.db 2023-05-14T06:24:45,169 copying build/lib/resources/quickumls/QuickUMLS_SAMPLE_lowercase_Windows_unqlite/umls-simstring.db/umls-terms.simstring.33.cdb -> build/bdist.linux-aarch64/wheel/resources/quickumls/QuickUMLS_SAMPLE_lowercase_Windows_unqlite/umls-simstring.db 2023-05-14T06:24:45,171 copying build/lib/resources/quickumls/QuickUMLS_SAMPLE_lowercase_Windows_unqlite/umls-simstring.db/umls-terms.simstring.40.cdb -> build/bdist.linux-aarch64/wheel/resources/quickumls/QuickUMLS_SAMPLE_lowercase_Windows_unqlite/umls-simstring.db 2023-05-14T06:24:45,174 copying build/lib/resources/quickumls/QuickUMLS_SAMPLE_lowercase_Windows_unqlite/language.flag -> build/bdist.linux-aarch64/wheel/resources/quickumls/QuickUMLS_SAMPLE_lowercase_Windows_unqlite 2023-05-14T06:24:45,176 copying build/lib/resources/quickumls/QuickUMLS_SAMPLE_lowercase_Windows_unqlite/README.md -> build/bdist.linux-aarch64/wheel/resources/quickumls/QuickUMLS_SAMPLE_lowercase_Windows_unqlite 2023-05-14T06:24:45,178 creating build/bdist.linux-aarch64/wheel/resources/quickumls/QuickUMLS_SAMPLE_lowercase_POSIX_unqlite 2023-05-14T06:24:45,180 creating build/bdist.linux-aarch64/wheel/resources/quickumls/QuickUMLS_SAMPLE_lowercase_POSIX_unqlite/cui-semtypes.db 2023-05-14T06:24:45,181 copying build/lib/resources/quickumls/QuickUMLS_SAMPLE_lowercase_POSIX_unqlite/cui-semtypes.db/semtypes.unqlite -> build/bdist.linux-aarch64/wheel/resources/quickumls/QuickUMLS_SAMPLE_lowercase_POSIX_unqlite/cui-semtypes.db 2023-05-14T06:24:45,184 copying build/lib/resources/quickumls/QuickUMLS_SAMPLE_lowercase_POSIX_unqlite/cui-semtypes.db/cui.unqlite -> build/bdist.linux-aarch64/wheel/resources/quickumls/QuickUMLS_SAMPLE_lowercase_POSIX_unqlite/cui-semtypes.db 2023-05-14T06:24:45,186 copying build/lib/resources/quickumls/QuickUMLS_SAMPLE_lowercase_POSIX_unqlite/database_backend.flag -> build/bdist.linux-aarch64/wheel/resources/quickumls/QuickUMLS_SAMPLE_lowercase_POSIX_unqlite 2023-05-14T06:24:45,188 copying build/lib/resources/quickumls/QuickUMLS_SAMPLE_lowercase_POSIX_unqlite/normalize-unicode.flag -> build/bdist.linux-aarch64/wheel/resources/quickumls/QuickUMLS_SAMPLE_lowercase_POSIX_unqlite 2023-05-14T06:24:45,190 copying build/lib/resources/quickumls/QuickUMLS_SAMPLE_lowercase_POSIX_unqlite/lowercase.flag -> build/bdist.linux-aarch64/wheel/resources/quickumls/QuickUMLS_SAMPLE_lowercase_POSIX_unqlite 2023-05-14T06:24:45,193 creating build/bdist.linux-aarch64/wheel/resources/quickumls/QuickUMLS_SAMPLE_lowercase_POSIX_unqlite/umls-simstring.db 2023-05-14T06:24:45,194 copying build/lib/resources/quickumls/QuickUMLS_SAMPLE_lowercase_POSIX_unqlite/umls-simstring.db/umls-terms.simstring.35.cdb -> build/bdist.linux-aarch64/wheel/resources/quickumls/QuickUMLS_SAMPLE_lowercase_POSIX_unqlite/umls-simstring.db 2023-05-14T06:24:45,196 copying build/lib/resources/quickumls/QuickUMLS_SAMPLE_lowercase_POSIX_unqlite/umls-simstring.db/umls-terms.simstring.37.cdb -> build/bdist.linux-aarch64/wheel/resources/quickumls/QuickUMLS_SAMPLE_lowercase_POSIX_unqlite/umls-simstring.db 2023-05-14T06:24:45,198 copying build/lib/resources/quickumls/QuickUMLS_SAMPLE_lowercase_POSIX_unqlite/umls-simstring.db/umls-terms.simstring.38.cdb -> build/bdist.linux-aarch64/wheel/resources/quickumls/QuickUMLS_SAMPLE_lowercase_POSIX_unqlite/umls-simstring.db 2023-05-14T06:24:45,200 copying build/lib/resources/quickumls/QuickUMLS_SAMPLE_lowercase_POSIX_unqlite/umls-simstring.db/umls-terms.simstring.39.cdb -> build/bdist.linux-aarch64/wheel/resources/quickumls/QuickUMLS_SAMPLE_lowercase_POSIX_unqlite/umls-simstring.db 2023-05-14T06:24:45,202 copying build/lib/resources/quickumls/QuickUMLS_SAMPLE_lowercase_POSIX_unqlite/umls-simstring.db/umls-terms.simstring.27.cdb -> build/bdist.linux-aarch64/wheel/resources/quickumls/QuickUMLS_SAMPLE_lowercase_POSIX_unqlite/umls-simstring.db 2023-05-14T06:24:45,204 copying build/lib/resources/quickumls/QuickUMLS_SAMPLE_lowercase_POSIX_unqlite/umls-simstring.db/umls-terms.simstring.14.cdb -> build/bdist.linux-aarch64/wheel/resources/quickumls/QuickUMLS_SAMPLE_lowercase_POSIX_unqlite/umls-simstring.db 2023-05-14T06:24:45,206 copying build/lib/resources/quickumls/QuickUMLS_SAMPLE_lowercase_POSIX_unqlite/umls-simstring.db/umls-terms.simstring.79.cdb -> build/bdist.linux-aarch64/wheel/resources/quickumls/QuickUMLS_SAMPLE_lowercase_POSIX_unqlite/umls-simstring.db 2023-05-14T06:24:45,209 copying build/lib/resources/quickumls/QuickUMLS_SAMPLE_lowercase_POSIX_unqlite/umls-simstring.db/umls-terms.simstring.8.cdb -> build/bdist.linux-aarch64/wheel/resources/quickumls/QuickUMLS_SAMPLE_lowercase_POSIX_unqlite/umls-simstring.db 2023-05-14T06:24:45,211 copying build/lib/resources/quickumls/QuickUMLS_SAMPLE_lowercase_POSIX_unqlite/umls-simstring.db/umls-terms.simstring.24.cdb -> build/bdist.linux-aarch64/wheel/resources/quickumls/QuickUMLS_SAMPLE_lowercase_POSIX_unqlite/umls-simstring.db 2023-05-14T06:24:45,213 copying build/lib/resources/quickumls/QuickUMLS_SAMPLE_lowercase_POSIX_unqlite/umls-simstring.db/umls-terms.simstring.43.cdb -> build/bdist.linux-aarch64/wheel/resources/quickumls/QuickUMLS_SAMPLE_lowercase_POSIX_unqlite/umls-simstring.db 2023-05-14T06:24:45,215 copying build/lib/resources/quickumls/QuickUMLS_SAMPLE_lowercase_POSIX_unqlite/umls-simstring.db/umls-terms.simstring.20.cdb -> build/bdist.linux-aarch64/wheel/resources/quickumls/QuickUMLS_SAMPLE_lowercase_POSIX_unqlite/umls-simstring.db 2023-05-14T06:24:45,217 copying build/lib/resources/quickumls/QuickUMLS_SAMPLE_lowercase_POSIX_unqlite/umls-simstring.db/umls-terms.simstring.120.cdb -> build/bdist.linux-aarch64/wheel/resources/quickumls/QuickUMLS_SAMPLE_lowercase_POSIX_unqlite/umls-simstring.db 2023-05-14T06:24:45,219 copying build/lib/resources/quickumls/QuickUMLS_SAMPLE_lowercase_POSIX_unqlite/umls-simstring.db/umls-terms.simstring.15.cdb -> build/bdist.linux-aarch64/wheel/resources/quickumls/QuickUMLS_SAMPLE_lowercase_POSIX_unqlite/umls-simstring.db 2023-05-14T06:24:45,222 copying build/lib/resources/quickumls/QuickUMLS_SAMPLE_lowercase_POSIX_unqlite/umls-simstring.db/umls-terms.simstring.28.cdb -> build/bdist.linux-aarch64/wheel/resources/quickumls/QuickUMLS_SAMPLE_lowercase_POSIX_unqlite/umls-simstring.db 2023-05-14T06:24:45,224 copying build/lib/resources/quickumls/QuickUMLS_SAMPLE_lowercase_POSIX_unqlite/umls-simstring.db/umls-terms.simstring.21.cdb -> build/bdist.linux-aarch64/wheel/resources/quickumls/QuickUMLS_SAMPLE_lowercase_POSIX_unqlite/umls-simstring.db 2023-05-14T06:24:45,226 copying build/lib/resources/quickumls/QuickUMLS_SAMPLE_lowercase_POSIX_unqlite/umls-simstring.db/umls-terms.simstring -> build/bdist.linux-aarch64/wheel/resources/quickumls/QuickUMLS_SAMPLE_lowercase_POSIX_unqlite/umls-simstring.db 2023-05-14T06:24:45,228 copying build/lib/resources/quickumls/QuickUMLS_SAMPLE_lowercase_POSIX_unqlite/umls-simstring.db/umls-terms.simstring.22.cdb -> build/bdist.linux-aarch64/wheel/resources/quickumls/QuickUMLS_SAMPLE_lowercase_POSIX_unqlite/umls-simstring.db 2023-05-14T06:24:45,230 copying build/lib/resources/quickumls/QuickUMLS_SAMPLE_lowercase_POSIX_unqlite/umls-simstring.db/umls-terms.simstring.30.cdb -> build/bdist.linux-aarch64/wheel/resources/quickumls/QuickUMLS_SAMPLE_lowercase_POSIX_unqlite/umls-simstring.db 2023-05-14T06:24:45,233 copying build/lib/resources/quickumls/QuickUMLS_SAMPLE_lowercase_POSIX_unqlite/umls-simstring.db/umls-terms.simstring.29.cdb -> build/bdist.linux-aarch64/wheel/resources/quickumls/QuickUMLS_SAMPLE_lowercase_POSIX_unqlite/umls-simstring.db 2023-05-14T06:24:45,235 copying build/lib/resources/quickumls/QuickUMLS_SAMPLE_lowercase_POSIX_unqlite/umls-simstring.db/umls-terms.simstring.31.cdb -> build/bdist.linux-aarch64/wheel/resources/quickumls/QuickUMLS_SAMPLE_lowercase_POSIX_unqlite/umls-simstring.db 2023-05-14T06:24:45,237 copying build/lib/resources/quickumls/QuickUMLS_SAMPLE_lowercase_POSIX_unqlite/umls-simstring.db/umls-terms.simstring.26.cdb -> build/bdist.linux-aarch64/wheel/resources/quickumls/QuickUMLS_SAMPLE_lowercase_POSIX_unqlite/umls-simstring.db 2023-05-14T06:24:45,239 copying build/lib/resources/quickumls/QuickUMLS_SAMPLE_lowercase_POSIX_unqlite/umls-simstring.db/umls-terms.simstring.17.cdb -> build/bdist.linux-aarch64/wheel/resources/quickumls/QuickUMLS_SAMPLE_lowercase_POSIX_unqlite/umls-simstring.db 2023-05-14T06:24:45,241 copying build/lib/resources/quickumls/QuickUMLS_SAMPLE_lowercase_POSIX_unqlite/umls-simstring.db/umls-terms.simstring.32.cdb -> build/bdist.linux-aarch64/wheel/resources/quickumls/QuickUMLS_SAMPLE_lowercase_POSIX_unqlite/umls-simstring.db 2023-05-14T06:24:45,244 copying build/lib/resources/quickumls/QuickUMLS_SAMPLE_lowercase_POSIX_unqlite/umls-simstring.db/umls-terms.simstring.33.cdb -> build/bdist.linux-aarch64/wheel/resources/quickumls/QuickUMLS_SAMPLE_lowercase_POSIX_unqlite/umls-simstring.db 2023-05-14T06:24:45,246 copying build/lib/resources/quickumls/QuickUMLS_SAMPLE_lowercase_POSIX_unqlite/umls-simstring.db/umls-terms.simstring.40.cdb -> build/bdist.linux-aarch64/wheel/resources/quickumls/QuickUMLS_SAMPLE_lowercase_POSIX_unqlite/umls-simstring.db 2023-05-14T06:24:45,248 copying build/lib/resources/quickumls/QuickUMLS_SAMPLE_lowercase_POSIX_unqlite/language.flag -> build/bdist.linux-aarch64/wheel/resources/quickumls/QuickUMLS_SAMPLE_lowercase_POSIX_unqlite 2023-05-14T06:24:45,250 copying build/lib/resources/quickumls/QuickUMLS_SAMPLE_lowercase_POSIX_unqlite/README.md -> build/bdist.linux-aarch64/wheel/resources/quickumls/QuickUMLS_SAMPLE_lowercase_POSIX_unqlite 2023-05-14T06:24:45,252 copying build/lib/resources/section_patterns.json -> build/bdist.linux-aarch64/wheel/resources 2023-05-14T06:24:45,255 creating build/bdist.linux-aarch64/wheel/tests 2023-05-14T06:24:45,256 copying build/lib/tests/test_medspacy.py -> build/bdist.linux-aarch64/wheel/tests 2023-05-14T06:24:45,258 copying build/lib/tests/__init__.py -> build/bdist.linux-aarch64/wheel/tests 2023-05-14T06:24:45,260 copying build/lib/tests/test_extensions.py -> build/bdist.linux-aarch64/wheel/tests 2023-05-14T06:24:45,262 copying build/lib/tests/test_notebooks.py -> build/bdist.linux-aarch64/wheel/tests 2023-05-14T06:24:45,263 running install_egg_info 2023-05-14T06:24:45,270 Copying medspacy.egg-info to build/bdist.linux-aarch64/wheel/medspacy-1.1.1a0-py3.9.egg-info 2023-05-14T06:24:45,281 running install_scripts 2023-05-14T06:24:45,299 creating build/bdist.linux-aarch64/wheel/medspacy-1.1.1a0.dist-info/WHEEL 2023-05-14T06:24:45,302 creating '/tmp/pip-wheel-b3mk8ui0/.tmp-0ezqob8i/medspacy-1.1.1a0-py3-none-any.whl' and adding 'build/bdist.linux-aarch64/wheel' to it 2023-05-14T06:24:45,304 adding 'medspacy/__init__.py' 2023-05-14T06:24:45,306 adding 'medspacy/_extensions.py' 2023-05-14T06:24:45,308 adding 'medspacy/_version.py' 2023-05-14T06:24:45,309 adding 'medspacy/components.py' 2023-05-14T06:24:45,310 adding 'medspacy/custom_tokenizer.py' 2023-05-14T06:24:45,312 adding 'medspacy/ner.py' 2023-05-14T06:24:45,313 adding 'medspacy/sentence_splitting.py' 2023-05-14T06:24:45,315 adding 'medspacy/util.py' 2023-05-14T06:24:45,317 adding 'medspacy/visualization.py' 2023-05-14T06:24:45,319 adding 'medspacy/common/__init__.py' 2023-05-14T06:24:45,320 adding 'medspacy/common/base_rule.py' 2023-05-14T06:24:45,322 adding 'medspacy/common/medspacy_matcher.py' 2023-05-14T06:24:45,324 adding 'medspacy/common/regex_matcher.py' 2023-05-14T06:24:45,326 adding 'medspacy/common/util.py' 2023-05-14T06:24:45,328 adding 'medspacy/context/__init__.py' 2023-05-14T06:24:45,330 adding 'medspacy/context/context.py' 2023-05-14T06:24:45,332 adding 'medspacy/context/context_graph.py' 2023-05-14T06:24:45,334 adding 'medspacy/context/context_modifier.py' 2023-05-14T06:24:45,336 adding 'medspacy/context/context_rule.py' 2023-05-14T06:24:45,338 adding 'medspacy/context/util.py' 2023-05-14T06:24:45,340 adding 'medspacy/io/__init__.py' 2023-05-14T06:24:45,341 adding 'medspacy/io/config_example.py' 2023-05-14T06:24:45,342 adding 'medspacy/io/db.py' 2023-05-14T06:24:45,344 adding 'medspacy/io/db_connect.py' 2023-05-14T06:24:45,345 adding 'medspacy/io/db_reader.py' 2023-05-14T06:24:45,347 adding 'medspacy/io/db_writer.py' 2023-05-14T06:24:45,349 adding 'medspacy/io/doc_consumer.py' 2023-05-14T06:24:45,350 adding 'medspacy/io/pipeline.py' 2023-05-14T06:24:45,352 adding 'medspacy/postprocess/__init__.py' 2023-05-14T06:24:45,354 adding 'medspacy/postprocess/postprocessing_functions.py' 2023-05-14T06:24:45,355 adding 'medspacy/postprocess/postprocessing_pattern.py' 2023-05-14T06:24:45,357 adding 'medspacy/postprocess/postprocessing_rule.py' 2023-05-14T06:24:45,358 adding 'medspacy/postprocess/postprocessor.py' 2023-05-14T06:24:45,360 adding 'medspacy/preprocess/__init__.py' 2023-05-14T06:24:45,362 adding 'medspacy/preprocess/preprocessing_rule.py' 2023-05-14T06:24:45,363 adding 'medspacy/preprocess/preprocessor.py' 2023-05-14T06:24:45,365 adding 'medspacy/section_detection/__init__.py' 2023-05-14T06:24:45,367 adding 'medspacy/section_detection/section.py' 2023-05-14T06:24:45,369 adding 'medspacy/section_detection/section_rule.py' 2023-05-14T06:24:45,372 adding 'medspacy/section_detection/sectionizer.py' 2023-05-14T06:24:45,373 adding 'medspacy/section_detection/util.py' 2023-05-14T06:24:45,375 adding 'medspacy/target_matcher/__init__.py' 2023-05-14T06:24:45,376 adding 'medspacy/target_matcher/concept_tagger.py' 2023-05-14T06:24:45,378 adding 'medspacy/target_matcher/target_matcher.py' 2023-05-14T06:24:45,380 adding 'medspacy/target_matcher/target_rule.py' 2023-05-14T06:24:45,384 adding 'resources/context_rules.json' 2023-05-14T06:24:45,387 adding 'resources/rush_rules.tsv' 2023-05-14T06:24:45,389 adding 'resources/section_patterns.json' 2023-05-14T06:24:45,391 adding 'resources/quickumls/QuickUMLS_SAMPLE_lowercase_POSIX_unqlite/README.md' 2023-05-14T06:24:45,392 adding 'resources/quickumls/QuickUMLS_SAMPLE_lowercase_POSIX_unqlite/database_backend.flag' 2023-05-14T06:24:45,394 adding 'resources/quickumls/QuickUMLS_SAMPLE_lowercase_POSIX_unqlite/language.flag' 2023-05-14T06:24:45,395 adding 'resources/quickumls/QuickUMLS_SAMPLE_lowercase_POSIX_unqlite/lowercase.flag' 2023-05-14T06:24:45,396 adding 'resources/quickumls/QuickUMLS_SAMPLE_lowercase_POSIX_unqlite/normalize-unicode.flag' 2023-05-14T06:24:45,398 adding 'resources/quickumls/QuickUMLS_SAMPLE_lowercase_POSIX_unqlite/cui-semtypes.db/cui.unqlite' 2023-05-14T06:24:45,400 adding 'resources/quickumls/QuickUMLS_SAMPLE_lowercase_POSIX_unqlite/cui-semtypes.db/semtypes.unqlite' 2023-05-14T06:24:45,403 adding 'resources/quickumls/QuickUMLS_SAMPLE_lowercase_POSIX_unqlite/umls-simstring.db/umls-terms.simstring' 2023-05-14T06:24:45,405 adding 'resources/quickumls/QuickUMLS_SAMPLE_lowercase_POSIX_unqlite/umls-simstring.db/umls-terms.simstring.120.cdb' 2023-05-14T06:24:45,406 adding 'resources/quickumls/QuickUMLS_SAMPLE_lowercase_POSIX_unqlite/umls-simstring.db/umls-terms.simstring.14.cdb' 2023-05-14T06:24:45,408 adding 'resources/quickumls/QuickUMLS_SAMPLE_lowercase_POSIX_unqlite/umls-simstring.db/umls-terms.simstring.15.cdb' 2023-05-14T06:24:45,409 adding 'resources/quickumls/QuickUMLS_SAMPLE_lowercase_POSIX_unqlite/umls-simstring.db/umls-terms.simstring.17.cdb' 2023-05-14T06:24:45,410 adding 'resources/quickumls/QuickUMLS_SAMPLE_lowercase_POSIX_unqlite/umls-simstring.db/umls-terms.simstring.20.cdb' 2023-05-14T06:24:45,412 adding 'resources/quickumls/QuickUMLS_SAMPLE_lowercase_POSIX_unqlite/umls-simstring.db/umls-terms.simstring.21.cdb' 2023-05-14T06:24:45,413 adding 'resources/quickumls/QuickUMLS_SAMPLE_lowercase_POSIX_unqlite/umls-simstring.db/umls-terms.simstring.22.cdb' 2023-05-14T06:24:45,415 adding 'resources/quickumls/QuickUMLS_SAMPLE_lowercase_POSIX_unqlite/umls-simstring.db/umls-terms.simstring.24.cdb' 2023-05-14T06:24:45,416 adding 'resources/quickumls/QuickUMLS_SAMPLE_lowercase_POSIX_unqlite/umls-simstring.db/umls-terms.simstring.26.cdb' 2023-05-14T06:24:45,418 adding 'resources/quickumls/QuickUMLS_SAMPLE_lowercase_POSIX_unqlite/umls-simstring.db/umls-terms.simstring.27.cdb' 2023-05-14T06:24:45,420 adding 'resources/quickumls/QuickUMLS_SAMPLE_lowercase_POSIX_unqlite/umls-simstring.db/umls-terms.simstring.28.cdb' 2023-05-14T06:24:45,421 adding 'resources/quickumls/QuickUMLS_SAMPLE_lowercase_POSIX_unqlite/umls-simstring.db/umls-terms.simstring.29.cdb' 2023-05-14T06:24:45,423 adding 'resources/quickumls/QuickUMLS_SAMPLE_lowercase_POSIX_unqlite/umls-simstring.db/umls-terms.simstring.30.cdb' 2023-05-14T06:24:45,425 adding 'resources/quickumls/QuickUMLS_SAMPLE_lowercase_POSIX_unqlite/umls-simstring.db/umls-terms.simstring.31.cdb' 2023-05-14T06:24:45,427 adding 'resources/quickumls/QuickUMLS_SAMPLE_lowercase_POSIX_unqlite/umls-simstring.db/umls-terms.simstring.32.cdb' 2023-05-14T06:24:45,428 adding 'resources/quickumls/QuickUMLS_SAMPLE_lowercase_POSIX_unqlite/umls-simstring.db/umls-terms.simstring.33.cdb' 2023-05-14T06:24:45,430 adding 'resources/quickumls/QuickUMLS_SAMPLE_lowercase_POSIX_unqlite/umls-simstring.db/umls-terms.simstring.35.cdb' 2023-05-14T06:24:45,431 adding 'resources/quickumls/QuickUMLS_SAMPLE_lowercase_POSIX_unqlite/umls-simstring.db/umls-terms.simstring.37.cdb' 2023-05-14T06:24:45,433 adding 'resources/quickumls/QuickUMLS_SAMPLE_lowercase_POSIX_unqlite/umls-simstring.db/umls-terms.simstring.38.cdb' 2023-05-14T06:24:45,434 adding 'resources/quickumls/QuickUMLS_SAMPLE_lowercase_POSIX_unqlite/umls-simstring.db/umls-terms.simstring.39.cdb' 2023-05-14T06:24:45,436 adding 'resources/quickumls/QuickUMLS_SAMPLE_lowercase_POSIX_unqlite/umls-simstring.db/umls-terms.simstring.40.cdb' 2023-05-14T06:24:45,438 adding 'resources/quickumls/QuickUMLS_SAMPLE_lowercase_POSIX_unqlite/umls-simstring.db/umls-terms.simstring.43.cdb' 2023-05-14T06:24:45,439 adding 'resources/quickumls/QuickUMLS_SAMPLE_lowercase_POSIX_unqlite/umls-simstring.db/umls-terms.simstring.79.cdb' 2023-05-14T06:24:45,441 adding 'resources/quickumls/QuickUMLS_SAMPLE_lowercase_POSIX_unqlite/umls-simstring.db/umls-terms.simstring.8.cdb' 2023-05-14T06:24:45,443 adding 'resources/quickumls/QuickUMLS_SAMPLE_lowercase_Windows_unqlite/README.md' 2023-05-14T06:24:45,444 adding 'resources/quickumls/QuickUMLS_SAMPLE_lowercase_Windows_unqlite/database_backend.flag' 2023-05-14T06:24:45,445 adding 'resources/quickumls/QuickUMLS_SAMPLE_lowercase_Windows_unqlite/language.flag' 2023-05-14T06:24:45,446 adding 'resources/quickumls/QuickUMLS_SAMPLE_lowercase_Windows_unqlite/lowercase.flag' 2023-05-14T06:24:45,447 adding 'resources/quickumls/QuickUMLS_SAMPLE_lowercase_Windows_unqlite/normalize-unicode.flag' 2023-05-14T06:24:45,450 adding 'resources/quickumls/QuickUMLS_SAMPLE_lowercase_Windows_unqlite/cui-semtypes.db/cui.unqlite' 2023-05-14T06:24:45,451 adding 'resources/quickumls/QuickUMLS_SAMPLE_lowercase_Windows_unqlite/cui-semtypes.db/semtypes.unqlite' 2023-05-14T06:24:45,454 adding 'resources/quickumls/QuickUMLS_SAMPLE_lowercase_Windows_unqlite/umls-simstring.db/umls-terms.simstring' 2023-05-14T06:24:45,456 adding 'resources/quickumls/QuickUMLS_SAMPLE_lowercase_Windows_unqlite/umls-simstring.db/umls-terms.simstring.120.cdb' 2023-05-14T06:24:45,457 adding 'resources/quickumls/QuickUMLS_SAMPLE_lowercase_Windows_unqlite/umls-simstring.db/umls-terms.simstring.14.cdb' 2023-05-14T06:24:45,459 adding 'resources/quickumls/QuickUMLS_SAMPLE_lowercase_Windows_unqlite/umls-simstring.db/umls-terms.simstring.15.cdb' 2023-05-14T06:24:45,460 adding 'resources/quickumls/QuickUMLS_SAMPLE_lowercase_Windows_unqlite/umls-simstring.db/umls-terms.simstring.17.cdb' 2023-05-14T06:24:45,461 adding 'resources/quickumls/QuickUMLS_SAMPLE_lowercase_Windows_unqlite/umls-simstring.db/umls-terms.simstring.20.cdb' 2023-05-14T06:24:45,463 adding 'resources/quickumls/QuickUMLS_SAMPLE_lowercase_Windows_unqlite/umls-simstring.db/umls-terms.simstring.21.cdb' 2023-05-14T06:24:45,464 adding 'resources/quickumls/QuickUMLS_SAMPLE_lowercase_Windows_unqlite/umls-simstring.db/umls-terms.simstring.22.cdb' 2023-05-14T06:24:45,466 adding 'resources/quickumls/QuickUMLS_SAMPLE_lowercase_Windows_unqlite/umls-simstring.db/umls-terms.simstring.24.cdb' 2023-05-14T06:24:45,467 adding 'resources/quickumls/QuickUMLS_SAMPLE_lowercase_Windows_unqlite/umls-simstring.db/umls-terms.simstring.26.cdb' 2023-05-14T06:24:45,469 adding 'resources/quickumls/QuickUMLS_SAMPLE_lowercase_Windows_unqlite/umls-simstring.db/umls-terms.simstring.27.cdb' 2023-05-14T06:24:45,470 adding 'resources/quickumls/QuickUMLS_SAMPLE_lowercase_Windows_unqlite/umls-simstring.db/umls-terms.simstring.28.cdb' 2023-05-14T06:24:45,472 adding 'resources/quickumls/QuickUMLS_SAMPLE_lowercase_Windows_unqlite/umls-simstring.db/umls-terms.simstring.29.cdb' 2023-05-14T06:24:45,474 adding 'resources/quickumls/QuickUMLS_SAMPLE_lowercase_Windows_unqlite/umls-simstring.db/umls-terms.simstring.30.cdb' 2023-05-14T06:24:45,475 adding 'resources/quickumls/QuickUMLS_SAMPLE_lowercase_Windows_unqlite/umls-simstring.db/umls-terms.simstring.31.cdb' 2023-05-14T06:24:45,477 adding 'resources/quickumls/QuickUMLS_SAMPLE_lowercase_Windows_unqlite/umls-simstring.db/umls-terms.simstring.32.cdb' 2023-05-14T06:24:45,478 adding 'resources/quickumls/QuickUMLS_SAMPLE_lowercase_Windows_unqlite/umls-simstring.db/umls-terms.simstring.33.cdb' 2023-05-14T06:24:45,480 adding 'resources/quickumls/QuickUMLS_SAMPLE_lowercase_Windows_unqlite/umls-simstring.db/umls-terms.simstring.35.cdb' 2023-05-14T06:24:45,482 adding 'resources/quickumls/QuickUMLS_SAMPLE_lowercase_Windows_unqlite/umls-simstring.db/umls-terms.simstring.37.cdb' 2023-05-14T06:24:45,483 adding 'resources/quickumls/QuickUMLS_SAMPLE_lowercase_Windows_unqlite/umls-simstring.db/umls-terms.simstring.38.cdb' 2023-05-14T06:24:45,485 adding 'resources/quickumls/QuickUMLS_SAMPLE_lowercase_Windows_unqlite/umls-simstring.db/umls-terms.simstring.39.cdb' 2023-05-14T06:24:45,486 adding 'resources/quickumls/QuickUMLS_SAMPLE_lowercase_Windows_unqlite/umls-simstring.db/umls-terms.simstring.40.cdb' 2023-05-14T06:24:45,488 adding 'resources/quickumls/QuickUMLS_SAMPLE_lowercase_Windows_unqlite/umls-simstring.db/umls-terms.simstring.43.cdb' 2023-05-14T06:24:45,489 adding 'resources/quickumls/QuickUMLS_SAMPLE_lowercase_Windows_unqlite/umls-simstring.db/umls-terms.simstring.79.cdb' 2023-05-14T06:24:45,491 adding 'resources/quickumls/QuickUMLS_SAMPLE_lowercase_Windows_unqlite/umls-simstring.db/umls-terms.simstring.8.cdb' 2023-05-14T06:24:45,493 adding 'tests/__init__.py' 2023-05-14T06:24:45,494 adding 'tests/test_extensions.py' 2023-05-14T06:24:45,496 adding 'tests/test_medspacy.py' 2023-05-14T06:24:45,497 adding 'tests/test_notebooks.py' 2023-05-14T06:24:45,499 adding 'medspacy-1.1.1a0.dist-info/LICENSE' 2023-05-14T06:24:45,500 adding 'medspacy-1.1.1a0.dist-info/METADATA' 2023-05-14T06:24:45,502 adding 'medspacy-1.1.1a0.dist-info/WHEEL' 2023-05-14T06:24:45,503 adding 'medspacy-1.1.1a0.dist-info/top_level.txt' 2023-05-14T06:24:45,505 adding 'medspacy-1.1.1a0.dist-info/RECORD' 2023-05-14T06:24:45,510 removing build/bdist.linux-aarch64/wheel 2023-05-14T06:24:45,657 Building wheel for medspacy (pyproject.toml): finished with status 'done' 2023-05-14T06:24:45,666 Created wheel for medspacy: filename=medspacy-1.1.1a0-py3-none-any.whl size=147946 sha256=c47ee5520fff0709f000a0c9c62cb3be3e4253c27f8e56ec51ff7e3679d20494 2023-05-14T06:24:45,668 Stored in directory: /tmp/pip-ephem-wheel-cache-zxklsdwd/wheels/f0/9d/f3/51d2f142845d56c6d57d12e51c0759e6f53548eab10a58e2e2 2023-05-14T06:24:45,684 Successfully built medspacy 2023-05-14T06:24:45,697 Removed build tracker: '/tmp/pip-build-tracker-8nq79i5y'