CU-8699mrvup docs: update urls throughout to point to new cogstack-nlp repo

README.md

@@ -2,7 +2,7 @@
 
 [![Build Status](https://github.com/CogStack/cogstack-nlp/actions/workflows/medcat-v2_main.yml/badge.svg?branch=main)](https://github.com/CogStack/cogstack-nlp/actions/workflows/medcat-v2_main.yml/badge.svg?branch=main)
 [![Documentation Status](https://readthedocs.org/projects/cogstack-nlp/badge/?version=latest)](https://readthedocs.org/projects/cogstack-nlp/badge/?version=latest)
-[![Latest release](https://img.shields.io/github/v/release/CogStack/MedCAT2)](https://github.com/CogStack/MedCAT2/releases/latest)
+[![Latest release](https://img.shields.io/github/v/release/CogStack/cogstack-nlp?filter=medcat/*)](https://github.com/CogStack/cogstack-nlp/releases/latest)
 <!-- [![pypi Version](https://img.shields.io/pypi/v/medcat.svg?style=flat-square&logo=pypi&logoColor=white)](https://pypi.org/project/medcat/) -->
 
 Cogstack Natural Language Processing is for analysing clinical data using AI to draw insights from text in or documents in an Electronic Health Records.

anoncat-demo-app/README.md

@@ -1,6 +1,6 @@
 # Deidentify app
 
-Demo for AnonCAT. It uses [MedCAT](https://github.com/CogStack/MedCAT), an advanced natural language processing tool, to identify and classify sensitive information, such as names, addresses, and medical terms.
+Demo for AnonCAT. It uses [MedCAT](https://github.com/CogStack/cogstack-nlp/tree/main/medcat-v1), an advanced natural language processing tool, to identify and classify sensitive information, such as names, addresses, and medical terms.
 
 ## Example
 
@@ -22,7 +22,7 @@ MODEL_NAME = '<NAME OF MODEL HERE.zip>'
 
 ### Build your own model
 
-To build your own models please follow the tutorials outlined in [MedCATtutorials](https://github.com/CogStack/MedCATtutorials)
+To build your own models please follow the tutorials outlined in [MedCATtutorials](https://github.com/CogStack/cogstack-nlp/tree/main/medcat-v1-tutorials)
 
 *__Note:__ This is currently under development*
 

anoncat-demo-app/app/frontend/src/App.vue

@@ -21,7 +21,7 @@
         <br>
         <p>Please DO NOT test with any real sensitive PHI data.</p>
         <br>
-        <p>Local validation and fine-tuning available via <a href="https://github.com/CogStack/MedCATtrainer">MedCATtrainer</a>.
+        <p>Local validation and fine-tuning available via <a href="https://github.com/CogStack/cogstack-nlp/tree/main/medcat-trainer">MedCATtrainer</a>.
           Email us, <a href="mailto:contact@cogstack.org">contact@cogstack.org</a>, to discuss model access, model performance, and your use case.
         </p>
         <br>

medcat-trainer/README.md

@@ -1,10 +1,9 @@
  # Medical <img src="https://github.com/CogStack/cogstack-nlp/blob/main/media/cat-logo.png?raw=true" width=45>oncept Annotation Tool Trainer
 
-[![Build Status](https://github.com/CogStack/cogstack-nlp/actions/workflows/medcat-trainer_ci.yml/badge.svg?branch=main)](https://github.com/CogStack/cogstack-nlp/actions/workflows/medcat-trainer_ci.yml?query=branch%3Amain)
 [![Build Status](https://github.com/CogStack/cogstack-nlp/actions/workflows/medcat-trainer_qa.yml/badge.svg?branch=main)](https://github.com/CogStack/cogstack-nlp/actions/workflows/medcat-trainer_qa.yml?query=branch%3Amain)
 [![Build Status](https://github.com/CogStack/cogstack-nlp/actions/workflows/medcat-trainer_release.yml/badge.svg)](https://github.com/CogStack/cogstack-nlp/actions/workflows/medcat-trainer_release.yml)
 [![Documentation Status](https://readthedocs.org/projects/cogstack-nlp-medcat-trainer/badge/?version=latest)](https://readthedocs.org/projects/cogstack-nlp-medcat-trainer/badge/?version=latest)
-[![Latest release](https://img.shields.io/github/v/release/CogStack/cogstack-nlp)](https://github.com/CogStack/cogstack-nlp/releases/latest)
+[![Latest release](https://img.shields.io/github/v/release/CogStack/cogstack-nlp?filter=medcat-trainer/*)](https://github.com/CogStack/cogstack-nlp/releases/latest)
 
 MedCATTrainer is an interface for building, improving and customising a given Named Entity Recognition
 and Linking (NER+L) model (MedCAT) for biomedical domain text.

medcat-trainer/docs/installation.md

@@ -4,8 +4,8 @@ MedCATtrainer is a docker-compose packaged Django application.
 ## Download from Dockerhub
 Clone the repo, run the default docker-compose file and default env var:
 ```shell
-$ git clone https://github.com/CogStack/MedCATtrainer
-$ cd MedCATtrainer
+$ git clone https://github.com/CogStack/cogstack-nlp
+$ cd cogstack-nlp/medcat-trainer
 $ docker-compose up
 ```
 
@@ -61,7 +61,7 @@ Environment variables are used to configure the app:
 
 |Parameter|Description|
 |---------|-----------|
-|MEDCAT_CONFIG_FILE|MedCAT config file as described [here](https://github.com/CogStack/MedCAT/blob/master/medcat/config.py)|
+|MEDCAT_CONFIG_FILE|MedCAT config file as described [here](https://github.com/CogStack/cogstack-nlp/blob/main/medcat-v2/medcat/config/config.py)|
 |BEHIND_RP| If you're running MedCATtrainer, use 1, otherwise this defaults to 0 i.e. False|
 |MCTRAINER_PORT|The port to run the trainer app on|
 |EMAIL_USER|Email address which will be used to send users emails regarding password resets|

medcat-trainer/docs/maintenance.md

@@ -6,7 +6,7 @@ be upgrading to the latest release.
 
 The latest stable releases update the `docker-compose.yml` and `docker-compose-prod.yml` files.
 
-To update these docker compose files, either copy them directly from the [repo](https://github.com/CogStack/MedCATtrainer)
+To update these docker compose files, either copy them directly from the [repo](https://github.com/CogStack/cogstack-nlp/tree/main/medcat-trainer)
 or update the cloned files via:
 
 ```shell

medcat-trainer/docs/project_admin.md

@@ -69,7 +69,7 @@ Admin users have extra options on the home screen:
 3. Save Model - Write the in memory model to disk - to save the current in memory model state. This option is generally not advised as full model training should be done outside the trainer instance ideally. 
 
 ### Notes
-- Example Concept and Vocab databses are freely available on MedCAT [github](https://github.com/CogStack/MedCAT).
+- Example Concept and Vocab databses are freely available on MedCAT [github](https://github.com/CogStack/cogstack-nlp/tree/main/medcat-v2).
 Note. UMLS and SNOMED-CT are licensed products so only these smaller trained concept / vocab databases are made available currently.
 - More documentation on the creation of UMLS / SNOMED-CT CDBs from respective source data will be released soon.
 - Tasks allow for the creation of meta-annotations and their associated set of values an annotator can use.

medcat-trainer/install.sh

@@ -7,8 +7,8 @@ DOCKER_COMP_FILE=dc.yml
 ENV_FILE=/tmp/mc_trainer/envs/env
 
 echo "Downloading docker-compose.yml and default env vars"
-curl https://cdn.githubraw.com/CogStack/MedCATtrainer/9fbd517e/docker-compose.yml > $DOCKER_COMP_FILE
-curl https://raw.githubusercontent.com/CogStack/MedCATtrainer/9fbd517e/envs/env > $ENV_FILE
+curl https://raw.githubusercontent.com/CogStack/cogstack-nlp/09e32429/medcat-trainer/docker-compose.yml > $DOCKER_COMP_FILE
+curl https://raw.githubusercontent.com/CogStack/cogstack-nlp/09e32429/medcat-trainer/envs/env > $ENV_FILE
 trap 'rm -rf /tmp/mc_trainer && cd $CURR_LOC' EXIT
 
 echo "Starting MedCATtrainer containers"

medcat-trainer/notebook_docs/API_Examples.ipynb

@@ -216,7 +216,7 @@
     "### Create CDBs and Vocabularies\n",
     "The MedCAT models used by MedCATTrainer are output by MedCAT instances of classesmedcat.cdb.CDB, medcat.utils.vocab.Vocabulary. Calling save_dict('\\<file location\\>') will write a file that can be loaded in another instance of MedCAT (via load_dict()), or within MedCATTrainer.\n",
     "\n",
-    "Examples models are provided on the MedCAT Repository: https://github.com/CogStack/MedCAT"
+    "Examples models are provided on the MedCAT Repository: https://github.com/CogStack/cogstack-nlp/tree/main/medcat-v1"
    ]
   },
   {

medcat-trainer/notebook_docs/Generate_CUI_Filters.ipynb

@@ -25,7 +25,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "Relation file from SNOMED-CT Preprocessing tutorial: https://github.com/CogStack/MedCATtutorials/blob/main/notebooks/specialised/Preprocessing_SNOMED_CT.ipynb, \n",
+    "Relation file from SNOMED-CT Preprocessing tutorial: https://github.com/CogStack/cogstack-nlp/blob/main/medcat-v1-tutorials/notebooks/specialised/Preprocessing_SNOMED_CT.ipynb, \n",
     "\n",
     "In section \"SNOMED Relationships\"\n"
    ]

medcat-trainer/notebook_docs/Processing_Annotations.ipynb

@@ -143,11 +143,11 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 2,
+   "execution_count": null,
    "metadata": {},
    "outputs": [],
    "source": [
-    "# Load the annotations downloaded - as described: https://github.com/CogStack/MedCATtrainer/blob/main/README.md#download-annos\n",
+    "# Load the annotations downloaded - as described: https://docs.cogstack.org/projects/medcat-trainer/en/latest/project_admin.html#downloading-annotations\n",
     "projs = json.load(open('example_data/MedCAT_Export_With_Text_2020-05-22_10_34_09.json'))['projects']"
    ]
   },

medcat-trainer/webapp/scripts/load_examples.py

@@ -61,7 +61,8 @@ def main(port=8000,
                     with open(vocab_tmp_file, 'wb') as f:
                         f.write(vocab_file.content)
                     print("Downloading example dataset")
-                    ds = requests.get('https://raw.githubusercontent.com/CogStack/MedCATtrainer/main/notebook_docs/example_data/ortho.csv')
+                    ds = requests.get(
+                        'https://raw.githubusercontent.com/CogStack/cogstack-nlp/09e32429/medcat-trainer/notebook_docs/example_data/ortho.csvv')
                     with open(dataset_tmp_file, 'w') as f:
                         f.write(ds.text)
 

medcat-v1/docs/main.md

@@ -33,7 +33,7 @@ A demo application is available at [MedCAT](https://medcat.sites.er.kcl.ac.uk).
 A guide on how to use MedCAT is available at [MedCAT Tutorials](https://github.com/CogStack/MedCATtutorials). Read more about MedCAT on [Towards Data Science](https://towardsdatascience.com/medcat-introduction-analyzing-electronic-health-records-e1c420afa13a).
 
 ## Related Projects
-- [MedCATtrainer](https://github.com/CogStack/MedCATtrainer/) - an interface for building, improving and customising a given Named Entity Recognition and Linking (NER+L) model (MedCAT) for biomedical domain text.
+- [MedCATtrainer](https://github.com/CogStack/cogstack-nlp/tree/main/medcat-trainer/) - an interface for building, improving and customising a given Named Entity Recognition and Linking (NER+L) model (MedCAT) for biomedical domain text.
 - [MedCATservice](https://github.com/CogStack/MedCATservice) - implements the MedCAT NLP application as a service behind a REST API.
 - [iCAT](https://github.com/CogStack/iCAT) - A docker container for CogStack/MedCAT/HuggingFace development in isolated environments.
 

medcat-v2-tutorials/README.md

@@ -6,25 +6,25 @@
 
 | Part | Title                                                                       |
 | ---- |-----------------------------------------------------------------------------|
-| 1.   |  [Migrate a v1 model to v2](https://github.com/CogStack/MedCATv2tutorials/blob/main/notebooks/introductory/migration/1._Migrate_v1_model_to_v2.ipynb)                                    |
+| 1.   |  [Migrate a v1 model to v2](https://github.com/CogStack/cogstack-nlp/blob/main/notebooks/introductory/migration/1._Migrate_v1_model_to_v2.ipynb)                                    |
 
 ### Basic (regex-tokenizer) tutorials
 
 | Part | Title                                                                       |
 | ---- |-----------------------------------------------------------------------------|
-| 1.   |  [Building a Concept Database and a Vocab](https://github.com/CogStack/MedCATv2tutorials/blob/main/notebooks/introductory/basic/1._Build_a_Concept_Database_and_a_Vocabulary.ipynb)                                    |
-| 2.   | [Unsupervised training on model](https://github.com/CogStack/MedCATv2tutorials/blob/main/notebooks/introductory/basic/2._Unsupervised_training_on_model.ipynb) |
-| 3.   | [Supervised training on model](https://github.com/CogStack/MedCATv2tutorials/blob/main/notebooks/introductory/basic/3._Supervised_training_on_model.ipynb) |
+| 1.   |  [Building a Concept Database and a Vocab](https://github.com/CogStack/cogstack-nlp/blob/main/notebooks/introductory/basic/1._Build_a_Concept_Database_and_a_Vocabulary.ipynb)                                    |
+| 2.   | [Unsupervised training on model](https://github.com/CogStack/cogstack-nlp/blob/main/notebooks/introductory/basic/2._Unsupervised_training_on_model.ipynb) |
+| 3.   | [Supervised training on model](https://github.com/CogStack/cogstack-nlp/blob/main/notebooks/introductory/basic/3._Supervised_training_on_model.ipynb) |
 
 ### MetaCAT (meta-annotation) tutorials
 
 | Part | Title                                                                       |
 | ---- |-----------------------------------------------------------------------------|
-| 1.   |  [Add a MetaCAT to a Model](https://github.com/CogStack/MedCATv2tutorials/blob/main/notebooks/introductory/meta/1._Add_a_MetaCat_to_a_Model.ipynb)                                    |
+| 1.   |  [Add a MetaCAT to a Model](https://github.com/CogStack/cogstack-nlp/blob/main/notebooks/introductory/meta/1._Add_a_MetaCat_to_a_Model.ipynb)                                    |
 
 ## Advanced tutorials
 
 | Part | Title                                                                       |
 | ---- |-----------------------------------------------------------------------------|
-| 1.   |  [Creating and using a custom tokenizer](https://github.com/CogStack/MedCATv2tutorials/blob/main/notebooks/advanced/1._Creating_and_using_a_custom_tokenizer.ipynb)                               |
-| 2.   |  [Create and use component](https://github.com/CogStack/MedCATv2tutorials/blob/main/notebooks/advanced/2._Create_and_use_component.ipynb)                                    |
+| 1.   |  [Creating and using a custom tokenizer](https://github.com/CogStack/cogstack-nlp/blob/main/notebooks/advanced/1._Creating_and_using_a_custom_tokenizer.ipynb)                               |
+| 2.   |  [Create and use component](https://github.com/CogStack/cogstack-nlp/blob/main/notebooks/advanced/2._Create_and_use_component.ipynb)                                    |