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Improved paragraph algorithm #118

Merged
merged 88 commits into from
Aug 1, 2024
Merged

Improved paragraph algorithm #118

merged 88 commits into from
Aug 1, 2024

Commits on Jan 9, 2023

  1. Merge branch 'master' of https://github.com/uclh-criu/miade into dev

    jenniferajiang committed Jan 9, 2023
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Commits on Jan 19, 2023

  1. update git tag versioning changes from #70

    jenniferajiang committed Jan 19, 2023
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Commits on Jan 31, 2023

  1. added confidence to meta to match for API compatibility

    jenniferajiang committed Jan 31, 2023
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Commits on Feb 1, 2023

  1. 🚨 Black

    jenniferajiang committed Feb 1, 2023
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  2. A little manual merge? added latest updated negex meta priority for t… 

    …esting
    jenniferajiang committed Feb 1, 2023
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Commits on Feb 17, 2023

  1. Merge branch 'feature/logging-config' into dev

    jenniferajiang committed Feb 17, 2023
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  2. Merge branch 'feature/logging-config' into dev

    jenniferajiang committed Feb 17, 2023
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  3. ✅ Updated tests

    jenniferajiang committed Feb 17, 2023
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  4. Merge branch 'feature/logging-config' into dev

    jenniferajiang committed Feb 17, 2023
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Commits on Feb 21, 2023

  1. Merge branch 'hotfix-negex-config' into dev

    jenniferajiang committed Feb 21, 2023
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Commits on Mar 3, 2023

  1. Merge branch 'feature/74-blacklist-filtering' into dev

    jenniferajiang committed Mar 3, 2023
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Commits on Mar 10, 2023

  1. Merge remote-tracking branch 'origin/feature/filter-debug-logs' into dev

    jenniferajiang committed Mar 10, 2023
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Commits on Apr 21, 2023

  1. Pull bug fixes and medcat upgrade: Merge branch 'master' of https://g… 

    …ithub.com/uclh-criu/miade into dev
    jenniferajiang committed Apr 21, 2023
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Commits on Apr 26, 2023

  1. Remove Debug Mode - Merge branch 'master' of https://github.com/uclh-… 

    …criu/miade into dev
    jenniferajiang committed Apr 26, 2023
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Commits on Apr 27, 2023

  1. Merge branch 'master' of https://github.com/uclh-criu/miade into dev

    jenniferajiang committed Apr 27, 2023
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Commits on Jul 27, 2023

  1. Merge branch 'feature/48-allergy-postprocessing' into dev

    jenniferajiang committed Jul 27, 2023
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  2. Merge branch 'master' of https://github.com/uclh-criu/miade into dev

    jenniferajiang committed Jul 27, 2023
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Commits on Jul 28, 2023

  1. Merge branch 'feature/48-allergy-postprocessing' into dev

    jenniferajiang committed Jul 28, 2023
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Commits on Sep 6, 2023

  1. Remove converted tag

    @jamesbrandreth
    jamesbrandreth committed Sep 6, 2023
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Commits on Sep 7, 2023

  1. ⬆️ Upgrade python to 3.11

    @jamesbrandreth
    jamesbrandreth committed Sep 7, 2023
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Commits on Sep 22, 2023

  1. ✨ paragraph chunking wip

    jenniferajiang committed Sep 22, 2023
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Commits on Sep 28, 2023

  1. Added loading regex config for paragraphs and capping problem concept… 

    …s to 10
    jenniferajiang committed Sep 28, 2023
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Commits on Sep 29, 2023

  1. Keep n dash between numbers, update tests

    jenniferajiang committed Sep 29, 2023
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  2. ✅

    jenniferajiang committed Sep 29, 2023
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  3. Merge branch 'feature/paragraph-chunking' into dev

    jenniferajiang committed Sep 29, 2023
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Commits on Oct 2, 2023

  1. 🐛🔊 Fixed negex bug and added logs for paragrapher

    jenniferajiang committed Oct 2, 2023
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Commits on Oct 4, 2023

  1. 🔊 Log message adjustments to make it more readable

    jenniferajiang committed Oct 4, 2023
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  2. 🏗️ Changed the way annotators and negex pipelines are configured - ad… 

    …ded options to disable pipelines
    jenniferajiang committed Oct 4, 2023
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  3. 🐛 Fixed historic concepts with no conversion are returned as is

    jenniferajiang committed Oct 4, 2023
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  4. ✅ forgot to commit updated tests

    jenniferajiang committed Oct 4, 2023
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Commits on Oct 5, 2023

  1. Added error handling for config loading

    jenniferajiang committed Oct 5, 2023
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Commits on Oct 6, 2023

  1. Merge branch 'bug-fix/negex-config-and-improve-logging' into dev

    jenniferajiang committed Oct 6, 2023
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  2. Merge branch 'master' of https://github.com/uclh-criu/miade into dev

    jenniferajiang committed Oct 6, 2023
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Commits on Oct 10, 2023

  1. ⬆️ MedCAT==1.9.3

    jenniferajiang committed Oct 10, 2023
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  2. Merge branch 'hotfix/medcat-patch' into dev

    jenniferajiang committed Oct 10, 2023
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  3. Merge branch 'master' of https://github.com/uclh-criu/miade into dev

    jenniferajiang committed Oct 10, 2023
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Commits on Oct 30, 2023

  1. Algorithm tweak to default to adverse reaction in allergy paragraphs (#… 

    …93)
    @jenniferjiangkells
    jenniferjiangkells authored Oct 30, 2023
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  2. 👷 Install pytorch cpu

    jenniferajiang committed Oct 30, 2023
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  3. Update lookup data (#94) 

    * 🗃️ Update latest lookup table data

* ✅ Update tests
    @jenniferjiangkells
    jenniferjiangkells authored Oct 30, 2023
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  4. 🐛 Fixed vtm deduplication bug (#96)

    @jenniferjiangkells
    jenniferjiangkells authored Oct 30, 2023
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  5. 👷 Run tests on dev PRs

    jenniferajiang committed Oct 30, 2023
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  6. 🐛 Fixed prob list cap bug to return exactly first 10 prob concepts

    jenniferajiang committed Oct 30, 2023
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  7. 🔧 Update sample miade config

    jenniferajiang committed Oct 30, 2023
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Commits on Nov 2, 2023

  1. Revert long problems list filtering and add numbering to problems list ( 

    #99)

* Revert long problems list capping - it was correct the way it was before

* ✨ Add numbering function to ProblemsAnnotator pipeline
    @jenniferjiangkells
    jenniferjiangkells authored Nov 2, 2023
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Commits on Nov 6, 2023

  1. Streamlit trainer preprocessing (#97) 

    * Added train csv preprocessing steps

* 🐛 Fixed train_csv document loading
    @jenniferjiangkells
    jenniferjiangkells authored Nov 6, 2023
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Commits on Nov 14, 2023

  1. Update problem blacklist

    jenniferajiang committed Nov 14, 2023
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  2. Merge branch 'update-blacklist' into dev

    jenniferajiang committed Nov 14, 2023
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  3. Update blacklist

    jenniferajiang committed Nov 14, 2023
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  4. Merge branch 'dev' of https://github.com/uclh-criu/miade into dev

    jenniferajiang committed Nov 14, 2023
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  5. Update blacklist

    jenniferajiang committed Nov 14, 2023
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Commits on Nov 15, 2023

  1. 🗃️ Update problems blacklist v2

    jenniferajiang committed Nov 15, 2023
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Commits on Nov 21, 2023

  1. Switch to Ruff for formatting and Linting (#104) 

    * Add ruff cache to gitignore

* 👷 Add Ruff to CI

* 👷 Set permitted line length to 100

* 🚨 ruff format

* 🚨 ruff lint

* Re-instate install test

* 🐛 Fix import cleanup regressions

* 🚨 ruff format
    @jamesbrandreth
    jamesbrandreth authored Nov 21, 2023
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Commits on Nov 23, 2023

  1. Merge branch 'blacklist' into dev

    @jamesbrandreth
    jamesbrandreth committed Nov 23, 2023
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Commits on Nov 29, 2023

  1. 🐛 Fix allergy_type and reaction filtering bug

    jenniferajiang committed Nov 29, 2023
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Commits on Nov 30, 2023

  1. Merge branch 'master' of https://github.com/uclh-criu/miade into bugf… 

    …ix/allergy-reactions-postprocess
    jenniferajiang committed Nov 30, 2023
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  2. Remove debug logging

    jenniferajiang committed Nov 30, 2023
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  3. Merge branch 'bugfix/allergy-reactions-postprocess' into dev

    jenniferajiang committed Nov 30, 2023
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  4. Remove (converted) tag

    jenniferajiang committed Nov 30, 2023
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  5. 🚚 Move lookup data outside package (#107) 

    * 🚚 Move lookup data outside package

* 🚚 Add lookup data to lookup_data/

* 🚨 ruff formatting
    @jenniferjiangkells
    jenniferjiangkells authored Nov 30, 2023
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Commits on Dec 18, 2023

  1. Merge branch 'master' of https://github.com/uclh-criu/miade into dev

    jenniferajiang committed Dec 18, 2023
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Commits on Jan 9, 2024

  1. Merge branch 'master' of https://github.com/uclh-criu/miade into dev

    jenniferajiang committed Jan 9, 2024
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Commits on Jan 17, 2024

  1. Put paragraph body in header (#111)

    @jenniferjiangkells
    jenniferjiangkells authored Jan 17, 2024
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Commits on Apr 22, 2024

  1. 🔧 Make paragraph regex configurable from lookup path (#117)

    @jenniferjiangkells
    jenniferjiangkells authored Apr 22, 2024
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  2. Merge branch 'dev' into improved-paragraph-algorithm

    jenniferajiang committed Apr 22, 2024
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Commits on Apr 23, 2024

  1. Super manual paragraph algorithm wip

    jenniferajiang committed Apr 23, 2024
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Commits on Jun 25, 2024

  1. wip

    @jenniferjiangkells
    jenniferjiangkells committed Jun 25, 2024
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  2. Fix ci - install with no deps

    @jenniferjiangkells
    jenniferjiangkells committed Jun 25, 2024
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  3. install med7 with requirements in ci

    @jenniferjiangkells
    jenniferjiangkells committed Jun 25, 2024
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  4. add requirements.txt

    @jenniferjiangkells
    jenniferjiangkells committed Jun 25, 2024
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  5. try find-links

    @jenniferjiangkells
    jenniferjiangkells committed Jun 25, 2024
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  6. try installing from wheel

    @jenniferjiangkells
    jenniferjiangkells committed Jun 25, 2024
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  7. try pip install directly

    @jenniferjiangkells
    jenniferjiangkells committed Jun 25, 2024
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  8. ci

    @jenniferjiangkells
    jenniferjiangkells committed Jun 25, 2024
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  9. Fix pip==24.0 in ci

    @jenniferjiangkells
    jenniferjiangkells committed Jun 25, 2024
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  10. note methods wip

    @jenniferjiangkells
    jenniferjiangkells committed Jun 25, 2024
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Commits on Jul 24, 2024

  1. Merge branch 'master' into improved-paragraph-algorithm

    @jenniferjiangkells
    jenniferjiangkells committed Jul 24, 2024
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  2. Add regex lookup back

    @jenniferjiangkells
    jenniferjiangkells committed Jul 24, 2024
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Commits on Jul 30, 2024

  1. Fixed lookup data loading

    @jenniferjiangkells
    jenniferjiangkells committed Jul 30, 2024
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  2. Added functions to merge paragraph and NumberedList object

    @jenniferjiangkells
    jenniferjiangkells committed Jul 30, 2024
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  3. Delete prose_paragraph attribute

    @jenniferjiangkells
    jenniferjiangkells committed Jul 30, 2024
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  4. Add docstrings

    @jenniferjiangkells
    jenniferjiangkells committed Jul 30, 2024
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  5. Added number list filter method in annotator

    @jenniferjiangkells
    jenniferjiangkells committed Jul 30, 2024
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  6. Fix tests

    @jenniferjiangkells
    jenniferjiangkells committed Jul 30, 2024
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Commits on Jul 31, 2024

  1. Cover edge cases and added tests

    @jenniferjiangkells
    jenniferjiangkells committed Jul 31, 2024
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  2. Add list_cleaner to annotator pipelines and make run_pipeline method … 

    …an abstract method
    @jenniferjiangkells
    jenniferjiangkells committed Jul 31, 2024
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  3. Add refine_paragraphs option to AnnotatorConfig

    @jenniferjiangkells
    jenniferjiangkells committed Jul 31, 2024
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  4. Added tests for new features

    @jenniferjiangkells
    jenniferjiangkells committed Jul 31, 2024
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Commits on Aug 1, 2024

  1. Fix docstring

    @jenniferjiangkells
    jenniferjiangkells committed Aug 1, 2024
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