Change Log#
All notable changes to this project will be documented in this file.
The format is based on Keep a Changelog and this project adheres to Semantic Versioning.
Unreleased#
1.7.1 - 2024-05-11#
Added#
Database count database methods in persistence layer.
Name to ID and ID to name transform methods for notes and sections.
Admission listing by note count.
Get note IDs by
hadm_id
and category.
Changes#
Fix admission existence checks.
1.7.0 - 2024-04-14#
Changed#
Upgrade to zensols.mednlp 1.7.0.
1.6.0 - 2024-02-27#
Added#
Better MIMIC paragraph chunker using additional features from zensols.nlp.
CLI action to remove cached files.
Changed#
Upgrade to zensols.mednlp 1.6.0.
1.5.2 - 2024-02-08#
Removed#
The zensols.dbpg dependency for PostgreSQL MIMIC-III DB access.
Changed#
SQLite is now the default database for MIMIC-III DB access. This removes this package zensols.mimicsid from needing the PostgreSQL driver from being install.
1.5.1 - 2024-01-17#
Changed#
Fix “missing
zensols.dbpg
package error” by pinning requirements to PostgreSQL db package as there is no clean way of separating the DB access logic without a large overhaul.
1.5.0 - 2023-12-05#
Changed#
Upgrade to zensols.mednlp version 1.5.0.
Fix SQLite admission ID types.
Added#
Support for Python 3.11.
Added note ID access for admissions.
Removed#
Support for Python 3.9.
1.4.3 - 2023-09-08#
Removed#
NoteFactor
’ssection
parameter has been removed in favor of creating default notes withcreate_default
. This is a lower risk change given how deep in the framework this class is used.
Added#
A new
DefaultNoteFactory
that always creates default/no-section notes.
Changed#
Faster note to admission ID resolution in database for faster preemptive note parsing.
NoteFactory.create_default
to create new default/no-section notes.
1.4.2 - 2023-08-25#
Changed#
Switch to
MultiProcessDefaultStash
, which allows for swapping in other multiprocessing implementations.
1.4.1 - 2023-08-16#
Changed#
PostreSQL is now optional, and to use it, the zensols.dbpg needs to be installed (see the README].
1.4.0 - 2023-08-15#
Downstream moderate risk update release.
Changes#
A cleaner CLI for MIMIC note access.
Default to section based
Note.write
.NoteStash
is now primed by upstream stashes for zensols.mimicsid MedSecId model install.Tokenzier separates on commas to find more MIMIC-III masks.
More MIMIC-III mask tags created and others regular expressions fixed.
Update to zensols.mednlp 1.4.0.
Added#
SQLite support for the MIMIC-III database.
Feature to clear cached notes from the
Corpus
class.CLI actions to write an admission to disk an to get random
hadm_ids
.
1.3.1 - 2023-06-25#
Changed#
Add default and settings for changing the MIMIC-III database name.
1.3.0 - 2023-06-20#
Changed#
Upgrade to zensols.mednlp 1.3.0.
1.2.0 - 2023-06-09#
Changed#
Upgrade to zensols.mednlp 1.2.0.
Move admission sample to
Admission
persister.Narrow body
FeatureDocument
s using right exclusive spans.
Added#
Note.annotator
property.Note
andAdmission
accessors toCorpus
container class.SQL
Note
counts.
1.1.0 - 2023-04-05#
Changed#
MIMIC notes write changes
Move application methods from
Corpus
to the application.Fixed procedure data to hospital admission class.
Changed#
Admission and note write semantics.
1.0.0 - 2023-02-02#
Changed#
Updated zensols.mednlp to 1.0.0.
0.1.1 - 2022-10-02#
Changed#
Upgrade dependencies.
0.1.0 - 2022-10-01#
Significant feature release.
Added#
Special MIMIC-III tokenization to deal with pseudo tokens.
Add spaCy
._.
token features extracted from MIMIC-III pseudo tokens.Combine zensols.mednlp document parser with MIMIC-III features.
Build out MIMIC-III container classes.
Add section and paragraph segmentation code and container classes.
Add reusable/shared data space for parsed documents.
Add Postgres database support.
0.0.1 - 2022-05-04#
Added#
Initial version.