Breaking changes compared to v1

There’s a number of breaking changes to the API compared to v1. This will attempt to list them all. If something was missed, don’t hesitate to create PR with the addition. Though do note, that only the major API-level changes will be listed.

API changes to CAT

Training

Training is now separated from the main CAT class into its own class (Trainer) and module (trainer.py). This affects the following methods (assumption is that cat is an instance of CAT):

v1 method	v2 method
`cat.train`	`cat.trainer.train_unsupervised`
`cat.train_supervised_raw`	`cat.trainer.train_supervised_raw`

Model saving

v1 method	v2 method
`cat.create_model_pack`	`cat.save_model_pack`

Removals

These methods were removed either due to a difference in approach or due to preceived unimportance. Protected (starting with _) or private (starting with __) methods won’t be recorded here. If you were previously relying on some of the behaviour provided by these, don’t hesitate to get in touch.

v1 method	Reason removed
`cat.train_supervised_from_json`	Don’t want to be tightly coupled to a file format here
`cat.multiprocessing_batch_char_size`	There is currently only one multiprocessing method
`cat.multiprocessing_batch_docs_size`	and that is `CAT.get_entities_multi_texts`
`cat.get_json`	Unclear usecases
`def destroy_pipe`	Unclear usecases

API Changes to CDB

The CDB class is now located in medcat.cdb.cdb module. However, it can be imported from the package directly as well, same as before (from medcat.cdb import CDB).

Names and CUIs are now mapped to variables differently

Instead of cui2<stuff> and name2stuff dicts, v2 provides cui2info and name2info mappings. Either of these have a dict that defines per concept or name information. Below you can see how to access the same things in the new version.

v1 method	v2 method	Notes
`cdb.cui2names[cui]`	`cdb.cui2info[cui]['names']`
`cdb.cui2snames[cui]`	`cdb.cui2info[cui]['subnames']`
`cdb.cui2count_train[cui]`	`cdb.cui2info[cui]['count_train']`
`cdb.cui2context_vectors[cui]`	`cdb.cui2info[cui]['context_vectors']`
`cdb.cui2type_ids[cui]`	`cdb.cui2info[cui]['type_ids']`
`cdb.cui2preferred_name[cui]`	`cdb.cui2info[cui]['preferred_name']`
`cdb.cui2average_confidence[cui]`	`cdb.cui2info[cui]['average_confidence']`
`cdb.name2cuis[name]`	`cdb.name2info[name]['per_cui_status'].keys()`	There’s no need to track per CUI status (on a per name basis) and per name CUIs separately
`cdb.name2cuis2status[name]`	`cdb.name2info[name]['per_cui_status']`
`cdb.name2count_train[name]`	`cdb.name2info[name]['count_train']`
`cdb.snames`	`cdb._subnames`
`cdb.make_stats()`	`cdb.get_basic_info()`

API changes for Config

Some config parts have been moved around for clarity. The below is the list of config parts that have been relocated. It must be noted that the ability to use config[path] = value was also removed.

v1 location	v2 location	Notes
`config.linking`	`config.components.linking`
`config.ner`	`config.components.ner`
`config.ner`	`config.components.ner`

Relocated packages / modules

Some packages and modules were relocated. We can see the list of relocations here.

v1 location	v2 location	Notes
`medcat.meta_cat`	`medcat.components.addons.meta_cat.meta_cat`
`medcat.utils.meta_cat`	`medcat.components.addons.meta_cat`
`medcat.config_meta_cat`	`medcat.config.config_meta_cat`
`medcat.cdb_maker`	`medcat.model_creation.cdb_maker`
`medcat.tokenizers.meta_cat_tokenizers`	`medcat.components.addons.meta_cat.mctokenizers.tokenizers`	All MetACAT stuff now here
`medcat.rel_cat`	`medcat.components.addons.relation_extraction.rel_cat`	All RelCAT stuff now here
`medcat.utils.relation_extraction.*`	`medcat.components.addons.relation_extraction.*`
`medcat.utils.ner.deid`	`medcat.components.ner.trf.deid`	Most DeID stuff now here
`medcat.utils.ner.model`	`medcat.components.ner.trf.model`
`medcat.utils.ner.helpers`	`medcat.components.ner.trf.helpers`
`medcat.tokenizer.transformers_ner`	`medcat.components.ner.trf.tokenizer`
`medcat.ner.transformers_ner`	`medcat.components.ner.tf.transformers_ner`
`medcat.datasets.transformers_ner`	`medcat.utils.ner.transformers_ner`
`medcat.datasets.data_collator`	`medcat.utils.ner.data_collator`