Merge pull request #1 from MicheleBortol/dev

Adds autoconfig

README.md

@@ -1,3 +1,7 @@
+![Badge_OMERO](https://github.com/MicheleBortol/omero-vitessce/actions/workflows/omero_plugin.yml/badge.svg)
+![Badge_PyPI](https://img.shields.io/pypi/v/omero-vitessce?label=pypi%20package)
+
+
 OMERO.omero_vitessce
 =======================
 
@@ -33,25 +37,74 @@ Add the omero web address (replace ´'"http://localhost:4080"'´ with your addre
 
 Now restart OMERO.web as normal for the configuration above to take effect.
 
+### omero-web-zarr
+While [omero-web-zarr](https://github.com/ome/omero-web-zarr) is not a requirement, but it is strongly recommended to have it installed and enabled for using this plugin
+omero-web-zarr is necessary to take advantage fully of the autogenerated config files for the Vitessce viewer,
+as they rely on omero-web-zarr to serve the images to the viewer.
+
+Please see https://pypi.org/project/omero-web-zarr/ for instructions on installing and enabling the omero-web-zarr plugin.
+
 Usage
 ============
-### Right-hand-side panel:
-- Prexisting config files
-- Autogenerating config file: COMING SOON!
 
+### Selecting the viewer
+The plugin can be used with:
+- `Vitessce` Tab on the right hand side panel.
+- `Open with` `->` `Vitessce` on the left side panel. 
+
+#### Right-hand-side panel:
+- **Prexisting config files**:  
+![Right-Config](https://github.com/user-attachments/assets/b8fea5f0-1d8f-4578-a577-8744d32dcaa5)   
+Clicking the link will open a new tab with the viewer displaying the selected configuration.
+- **Autogenerating config file**:  
+![Right-Auto](https://github.com/user-attachments/assets/8dfa22cc-dbb5-493d-b837-d609a11a1346)  
+Clicking the button will autogenerate a config file and attach it to the dataset/image, and the viewer displaying the autogenerated configuration.  
 
-### Open-with:
-Right click on `projects`, `datasets` or `images` in the left-panel and select `open-witch` -> `Vitessce`.  
+#### Open-with:
+Right click on a `dataset` or an `images` in the left-panel and select `open-with` -> `Vitessce`.  
 This will open the vitessce viewer in a new tab using the first configuration file attachement.
+![Openwith-image](https://github.com/user-attachments/assets/f75cc27c-4cd3-4a19-ae20-7d8f0a47aa87)
+
+### Viewer window
+After using a The Vitessce viewer is opened in a new tab:
+![image](https://github.com/user-attachments/assets/77de517e-67e4-42d6-a2b6-2a3a6a11dc7e)
+
+### Config files
+The omero-vitessce plugin considers all files with the `.json.txt` extension attached to the image or dataset as config files for the viewer.
+The config files should follow the vitessce view-config-json format: http://vitessce.io/docs/view-config-json/
+
+#### Autogenerated config files
+Config files can be autogenerated for:
+- `images`: A spatial view and a layer controller view are setup for the image.
+- `datasets`: All images in the dataset are bundled togheter and a spatial view and a layer controller are setup.
+
+Assumes that the images are in the OME-NGFF format v0.4 and that [omero-web-zarr](https://github.com/ome/omero-web-zarr) is
+available to serve the images.
+
+#### Custom config files
+Custom config files should have a `.json.txt` extension and added as attachements to a dataset or an image.
+The configuration files does not need to refer to the dataset / image it is attached to and can refer to other images.
+
+
+[examples](http://vitessce.io/examples/)
+
+#### Serving the images / data /metadata
+Images and data can be served through:
+- [omero-web-zarr](https://pypi.org/project/omero-web-zarr/):  OME-NGFF images only.
+- [omero-openlink](https://github.com/sukunis/OMERO.openlink): all images and file attachements.
+- ´webclient/annotation/´ endpoint: only for Annotations (useful for file attachments).
 
 Development
 =======================
 
 ## Sources
 
+The main sources are:
 - cookiecutter-omero-webapp: https://github.com/ome/cookiecutter-omero-webapp
 - `react_webapp` from omero-web-apps-examples: https://github.com/ome/omero-web-apps-examples/tree/master/react-webapp
-- Vitessce python package (will be used for generating config files) http://python-docs.vitessce.io/
+- Vitessce python package used for generating config files http://python-docs.vitessce.io/
+- omero-web-zarr to serve OME-NGFF images: https://github.com/ome/omero-web-zarr
+- omero-openlink to serve images and other files: https://github.com/sukunis/OMERO.openlink
 
 ## React web app
 
@@ -97,9 +150,9 @@ You also need to install the app into your `omero-web` environment:
 
 You will need to have the app configured in your OMERO.web install:
 
-    $  omero config append omero.web.apps '"omero_vitessce"'
+    $ omero config append omero.web.apps '"omero_vitessce"'
     $ omero config append omero.web.ui.right_plugins '["Vitessce", "omero_vitessce/webclient_plugins/right_plugin.vitessce.js.html", "vitessce_tab"]'
-    $  omero config set omero.web.omero_vitessce.serveraddress '"http://localhost:4080"'
+    $ omero config set omero.web.omero_vitessce.serveraddress '"http://localhost:4080"'
 
 It bundles React in production mode and optimizes the build for the best performance.
 

omero_vitessce/__init__.py

@@ -1,16 +0,0 @@
-#
-# Copyright (c) 2019 University of Dundee.
-#
-# This program is free software: you can redistribute it and/or modify
-# it under the terms of the GNU Affero General Public License as
-# published by the Free Software Foundation, either version 3 of the
-# License, or (at your option) any later version.
-#
-# This program is distributed in the hope that it will be useful,
-# but WITHOUT ANY WARRANTY; without even the implied warranty of
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-# GNU Affero General Public License for more details.
-#
-# You should have received a copy of the GNU Affero General Public License
-# along with this program.  If not, see <http://www.gnu.org/licenses/>.
-#

omero_vitessce/omero_vitessce_settings.py

@@ -3,6 +3,8 @@
 
 
 def str_not_empty(o):
+    """Checks for empty/invalid strings.
+    """
     s = str(o)
     if not o or not s:
         raise ValueError('Invalid empty value')

omero_vitessce/templates/omero_vitessce/vitessce_panel.html

@@ -7,15 +7,19 @@
 		</body>
 			{% if json_configs %}
 				<div class="right_tab_inner">
-					<p>Please select a config file or clic "Auto" to autogenerate one.</p>
+					<p>Please select an attached config file from the list below:</p>
 					{% for file, url in json_configs.items%}
-						<a href={{url}}> {{file}}</a>
+						<a href={{url}} target="_blank"> {{file}}</a>
 					{% endfor %}
 				</div>
 			{% else %}
 				<div class="right_tab_inner">
 					<p> There are no config files attached! </p>
 					<p> Either attach a config file or click below to autogenerate one:</p>
+					<button type="button">
+						<a href="{% url 'generate_config' %}/{{obj_type}}/{{obj_id}}";>Generate Config File</a>
+					</button>
+
 				</div>
 			{% endif %}
 		</body>

omero_vitessce/templates/omero_vitessce/webclient_plugins/right_plugin.vitessce.js.html

@@ -4,7 +4,7 @@
 $(document).ready(function() {
 
     $("#vitessce_tab").omeroweb_right_plugin({
-        supported_obj_types: ['project','dataset','image'],
+        supported_obj_types: ['dataset','image'],
         load_plugin_content: function(selected, obj_dtype, obj_id) {    // Url based on selected object(s)
             var url = '{% url 'vitessce_tab' %}' + obj_dtype + '/' + obj_id + '/';
             $(this).load(url);

omero_vitessce/urls.py

@@ -1,25 +1,16 @@
-#
-# Copyright (c) 2017 University of Dundee.
-#
-# This program is free software: you can redistribute it and/or modify
-# it under the terms of the GNU Affero General Public License as
-# published by the Free Software Foundation, either version 3 of the
-# License, or (at your option) any later version.
-#
-# This program is distributed in the hope that it will be useful,
-# but WITHOUT ANY WARRANTY; without even the implied warranty of
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-# GNU Affero General Public License for more details.
-#
-# You should have received a copy of the GNU Affero General Public License
-# along with this program.  If not, see <http://www.gnu.org/licenses/>.
-#
-
 from django.urls import re_path
 
 from . import views
 
 urlpatterns = [
+    # Generate config Button
+    re_path(r"^generate_config/(?P<obj_type>[a-z]+)/(?P<obj_id>[0-9]+)",
+            views.generate_config, name='generate_config'),
+
+    # Button placeholder
+    re_path(r"^generate_config$", views.vitessce_index,
+            name="generate_config"),
+
     # Right panel plugin
     re_path(r"(?P<obj_type>[a-z]+)/(?P<obj_id>[0-9]+)",
             views.vitessce_panel, name='vitessce_tab'),