📝 Update documentation

.github/ISSUE_TEMPLATE/bug_report.md

@@ -0,0 +1,29 @@
+---
+name: Bug report
+about: Create a report to help us improve
+
+---
+
+**Describe the bug**
+A clear and concise description of what the bug is.
+
+**To Reproduce**
+Steps to reproduce the behavior:
+1. Go to '...'
+2. Click on '....'
+3. Scroll down to '....'
+4. See error
+
+**Expected behavior**
+A clear and concise description of what you expected to happen.
+
+**Screenshots**
+If applicable, add screenshots to help explain your problem.
+
+**Please complete the following information:**
+ - Version: [see bottom of the browser screen]
+ - OS: [e.g. Windows, Linux, OS X]
+ - Browser: [e.g. chrome, safari, firefox]
+
+**Additional context**
+Add any other context about the problem here.

.github/ISSUE_TEMPLATE/documentation_request.md

@@ -0,0 +1,9 @@
+---
+name: Documentation request
+about: Suggest an idea to enhance documentation
+
+---
+
+**What kind of information do you search? Please describe.** 
+
+**Describe the solution you'd like**

.github/ISSUE_TEMPLATE/feature_request.md

@@ -0,0 +1,17 @@
+---
+name: Feature request
+about: Suggest an idea for this project
+
+---
+
+**Is your feature request related to a problem? Please describe.**
+A clear and concise description of what the problem is. 
+
+**Describe the solution you'd like**
+A clear and concise description of what you want to happen.
+
+**Describe alternatives you've considered**
+A clear and concise description of any alternative solutions or features you've considered.
+
+**Additional context**
+Add any other context or screenshots about the feature request here.

.github/ISSUE_TEMPLATE/refactoring.md

@@ -0,0 +1,11 @@
+---
+name: Refactoring (for developers)
+about: Refactor the application
+
+---
+
+**Describe the refactoring action**
+A clear and concise description of what the action is.
+
+**Expected benefit**
+A clear and concise description of what you expect to improve by the refactoring.

CITATION.CFF

@@ -0,0 +1,10 @@
+cff-version: 1.2.0
+message: "If you use this software, please cite it as below."
+authors:
+- family-names: "Terriel"
+  given-names: "Lucas"
+  orcid: "https://orcid.org/0000-0002-9189-258X"
+title: "Semantic@"
+version: 0.0.1
+date-released: 2022-05-5
+url: "https://github.com/Lucaterre/semanticat"

README.md

@@ -1,24 +1,31 @@
 <!--<img src="" width=300 align=right>-->
 
 ![Python Version](https://img.shields.io/badge/python-3.8-blue) [![MIT License](https://img.shields.io/apm/l/atomic-design-ui.svg?)](https://github.com/tterb/atomic-design-ui/blob/master/LICENSEs) [![Semantic@ CI build](https://github.com/Lucaterre/semanticat/actions/workflows/CI.yml/badge.svg)](https://github.com/Lucaterre/semanticat/actions/workflows/CI.yml)
-<!-- CI badge -->
+
+
 # Semanti🐱 
 
+----
+
 **WORK-IN-PROGRESS**
 
-Semantic@ is a platform for enriching XML documents in TEI or EAD format with named entities. 
+Semantic@ is a semantic annotation platform for enriching XML documents in [TEI](https://tei-c.org/) or [EAD](https://www.loc.gov/ead/) schemas with semantic annotations.
 
-After importing the document(s), apply the NER model and correct prediction or annotate manually from-zero and finally export and/or publish your XML with annotations inside.
+Follow a simple workflow: After importing the document(s), apply the NER model and correct prediction or annotate manually from-zero and finally export and/or publish your XML with annotations directly inside.
 
+This platform is also designed to adapt generically to the diversity of publishing projects and a base for adding custom components.
 
-## :battery: Installation
 
+## :movie_camera: Demo
 
+![semanticat_demo](./documentation/semanticat_demo.gif)
+
+## :battery: Installation
 
 1. Clone the Github repository
 
 ```bash
-git clone 
+git clone https://github.com/Lucaterre/semanticat.git
 ```
 
 2. Move inside the directory
@@ -48,6 +55,8 @@ pip install -r requirements.txt
 
 ## :rocket: Run Locally
 
+:fire: This application is intended to be simple and local for the moment. **Please note that the application is currently optimized for the Firefox browser.**
+
 Use the semantic@ CLI; inside the `semanticat/` directory, launch the command :
 
 ```bash
@@ -56,52 +65,85 @@ python run.py
 
 Others arguments :
 
-| **Type**              | **Details**                                  |
-|-----------------------|----------------------------------------------|
-| `--dev_mode`          | Launch app in development mode               |
+| **Type**              | **Details**                              |
+|-----------------------|------------------------------------------|
+| `--dev_mode`          | Launch application in development mode   |
 | `--erase_recreate_db` | Clean and Restore all database :warning: |
 
-## :arrow_forward: Quick Start
 
-(TODO : créer un wiki ? avec détails sur les exports, sur la manière d'annoter, sur comment enregistrer sur modèle NER etc.)
+## :arrow_forward: Getting started
+
+
+- Start by creating a project with the button `Create a new project` and open your project;
+- Go to `Menu` > `Manage documents` and import your XML, now you can see your documents in
+`Project workflow` view (You can mix EAD and TEI);
+- In `Project workflow` view: Apply `parse` feature on document one by one or apply `Parse All` on all documents;
+
+- Go to `Menu` > `configuration`, two use cases :
+
+1. You don't want to apply a NER model, and you want to manually annotate your data :
+- First, define Annotation mapping (see the "Mapping details" section);
+- Add labels with `Add new pair to mapping scope`;
+- Then, go to `Project workflow` > `correct named entities` and start annotation.
+
+2. You want to use an NER (recommend) model to predict named entities and correct afterwards (see the "NER configuration details" section):
+- First, select checkbox `NER Recommenders`;
+- Then, Choose the correct language that corresponding to your model;
+- Then, Select the model and save;
+- Wait, the pre-mapping appears, you can then adapt it (see the "Mapping details" section);
+- Go to `Project workflow` > `Launch Ner` (or `Launch Ner on all`);
+- When the process is complete,s, go to `correct named entities` and correct the predictions or add annotations.
+
+- Whatever the chosen scenario, once the correction is finished, you can export your document (see the "Export details" section) !
+
+## Detail sections
+
+### Mapping
 
-- Start by "create a new project"
-- Go to "Menu" > "Manage documents" and import your XML, You can see your documents in
-"Project workflow" view
-- Apply "parse" on document one by one or apply "parse" on all documents
-- Go to "Menu" > "configuration", two use cases :
+The mapping is a table that references the labels you use for annotation with:
 
-1. You don't apply NER model, and use semantic@ to create manually annotated data :
-- First, define Annotation mapping ("NER Label" is display on annotation view, "Prefered index label" is display in export, define color) and save everytime
-- Then, go to "Project workflow" > "correct named entities" and start annotate
+- *Ner Label*: The default label use to annotate or use by your model;
+- *Prefered Index label*: The label that will appear in the output;
+- *Color*: label color in annotation view.
 
-2. You want to use NER recommenders to predict named entities (see the "NER configuration details section"):
-- First, select checkbox 'NER Recommenders'
-- then, Choose the language that corresponding to your model
-- then, Select the model and save
-- Adjust the mapping
-- Go to "Project workflow" > "Launch Ner"
-- After the process, go to "correct named entities" to correct the predictions
+You can add new labels to your existing schema via `Add new pair to mapping scope`.
 
-- Now you can export your document !
+Be careful if you remove a label from table, if your model has already made predictions or if you have started to correct document, all annotations will be destroyed.
 
-## NER configuration details section
+### NER configuration
 
-The NER framework that semantic@ use is SpaCy.
+Currently, Semantic@ uses the NER SpaCy framework, in the future other frameworks may be integrated.
 
-By default, the platform provides two small pre-trained model for French and English.
+When installing the Semantic@, two pre-trained models for French (fr_core_news_sm) and English (en_core_web_sm) are already available
 
-For add new [SpaCy pre-trained model](https://spacy.io/usage/models) : 
+For add a new available [SpaCy pre-trained model](https://spacy.io/usage/models), before starting Semantic@, launch in terminal : 
 
 ```bash
 python -m spacy download <name-pretrained-model>
 ```
 
-The SpaCy pre-trained language are sometimes slow and too generic for your data, you 
-can use your own trained model, place your NER model folder under `/instance_config/my_features/my_models/` 
+The new pre-trained model will be directly available in model list from `configuration`.
+
+Sometimes, SpaCy’s default in-built pre-trained NER model are too slow and too generic for your data (the model is far from perfect so it doesn't necessarily detect your labels).
+If you have training a better statistical NER model with SpaCy, you can place your NER model folder under `/instance_config/my_features/my_models/` 
+
+Your model will be directly available in model list from `configuration`.
+
+### Export
+
+There are different XML export solutions : 
+
+- `annotations inline (based on characters offsets)` (TEI specific): This export uses standoff converter and uses the positions of annotations in the text to produce output. It is precise but sometimes it takes time.
+- `annotations to controlaccess level` (EAD specific): This export tags annotations in a level of type <controlaccess>.
+- `annotations inline (based on surface form matching)` (TEI & EAD): This export uses the surface shape of annotated mentions to tag the output. It is fast but sometimes less precise.
+
+
+- `annotations in JSON`: This export allows you to keep track of your annotations in a JSON format and import it directly into the annotation view.
 
 ## :crying_cat_face: Bug reports
 
+Feel free to create a new issue (new features, bug reports, documentation etc.).
+
 ## :computer: Stack 
 
 ### Interface
@@ -112,8 +154,26 @@ can use your own trained model, place your NER model folder under `/instance_con
 
 ### Main Components
 
-## :bust_in_silhouette: Authors
+- [![Spacy](https://img.shields.io/badge/NLP%20with-SpaCy-blue)](https://spacy.io/)
+
+- [![RecogitoJS](https://img.shields.io/badge/Text%20annotation%20with-RecogitoJS-9cf)](https://github.com/recogito/recogito-js)
+
+- [![Standoffconverter](https://img.shields.io/badge/Annotations%20in%20TEI%20with-StandoffConverter-red)](https://github.com/standoff-nlp/standoffconverter)
+
+## :bust_in_silhouette: Mainteners
 
 - [@Lucaterre](https://github.com/Lucaterre)
 
+
+## How to cite
+
+Please use the following citation:
+
+    @misc{terriel-2022-semanticat,
+        title = "Semantic@ : a semantic annotation platform for enriching XML documents in TEI or EAD schemas with semantic annotations.",
+        author = "Terriel, Lucas",
+        year = "2022",
+        url = "https://github.com/Lucaterre/semanticat",
+    }
+
 [![forthebadge made-with-python](http://ForTheBadge.com/images/badges/made-with-python.svg)](https://www.python.org/)

app/views/projectHandler.py

@@ -6,7 +6,8 @@
                    redirect,
                    render_template,
                    flash,
-                   abort)
+                   abort,
+                   url_for)
 
 from app.config import (app,
                         db)
@@ -36,8 +37,6 @@ def index():
                 db.session.commit()
                 flash(f'New project {project_name} created now.',
                       category='success')
-                return render_template('main/project.edition.html',
-                                       projects=Project.return_all_projects())
         else:
             flash('Project always exist ! Please change the name.', category='warning')
     return render_template('main/project.edition.html',
@@ -53,6 +52,6 @@ def remove_project(project_id):
         db.session.delete(project)
         db.session.commit()
         flash(f'Project : {project.project_name} completely removed.', category='warning')
-        return redirect("/"), 200
+        return redirect(url_for('index'))
     else:
         abort(404, description="Project not found")