Idr front page

.bumpversion.cfg

@@ -17,4 +17,4 @@ values =
 
 [bumpversion:part:build]
 
-[bumpversion:file:setup.py]
+[bumpversion:file:idr_gallery/version.py]

.gitignore

@@ -3,4 +3,3 @@
 dist
 omero_gallery.egg-info
 .omero
-node_modules/

MANIFEST.in

@@ -1,3 +1,3 @@
 include README.rst
 include LICENSE
-recursive-include omero_gallery *
+recursive-include idr_gallery *

README.rst

@@ -4,8 +4,8 @@
 .. image:: https://badge.fury.io/py/omero-gallery.svg
     :target: https://badge.fury.io/py/omero-gallery
 
-OMERO.gallery
-=============
+IDR gallery
+===========
 
 This is an OMERO.web plugin (Django app) that provides a 'gallery' view of images in OMERO, ideal for public browsing without editing.
 
@@ -25,65 +25,21 @@ Install the app using `pip <https://pip.pypa.io/en/stable/>`_:
 
 ::
 
-    $ pip install -U omero-gallery
+    $ pip install -U idr-gallery
 
 Add gallery custom app to your installed web apps:
 
 ::
 
-    $ omero config append omero.web.apps '"omero_gallery"'
+    $ omero config append omero.web.apps '"idr_gallery"'
 
 Now restart OMERO.web as normal.
 
 
-OMERO.gallery overview
-======================
-
-This application supports 2 alternative views of your data in OMERO, which can
-be chosen and customised via config settings:
-
-* Default UI (no config): Browse `Group > Project > Dataset > Image`
-* Categories UI: Show categories of interest. Allow filtering by map annotations.
-
-For both views, public access can be enabled
-`as described here <https://docs.openmicroscopy.org/latest/omero/sysadmins/public.html>`_,
-otherwise users will see the standard web login screen.
-Once logged-in (as a regular user or public user), the data displayed will
-include all data accessible to that user via the normal OMERO permissions.
-
-
-Default UI
-----------
-
-This view supports minimal functionality required for browsing the hierarchy
-from Groups -> Projects -> Datasets -> Images. Screen/Plate/Well data is
-not supported in this UI.
-
-The home page will display all the available groups that the user can access, with a random
-thumbnail from each group. The number of Projects, Datasets and Images within each group
-will also be displayed.
-
-.. image:: https://ome.github.io/omero-gallery/images/gallery.png
-
-
-On browsing into a group, the Projects and 'orphaned' Datasets will be shown in a similar layout.
-
-.. image:: https://ome.github.io/omero-gallery/images/show_group.png
-
-Projects are shown with 5 thumbnails from each Dataset. Clicking 'All Images' will load all the remaining thumbnails
-from a chosen Dataset (or you can browse to the Dataset itself by clicking the Dataset name link).
-
-.. image:: https://ome.github.io/omero-gallery/images/show_project.png
-
-Clicking a thumbnail will take you directly to the full image viewer.
-
-.. image:: https://ome.github.io/omero-gallery/images/webgateway_viewer.png
-
-
-Categories UI
--------------
+IDR.gallery overview
+====================
 
-This view was originally developed for use in the IDR and can be seen at
+This UI was developed for use in the IDR and can be seen at
 https://idr.openmicroscopy.org/. In the IDR, a "Study" is a Project or Screen
 and they are annotated with Key-Value data in the form of Map Annotations,
 for example ``Study Type: 3D-tracking``.
@@ -98,8 +54,8 @@ https://github.com/ome/omero-mapr/ is installed then you can:
 * Find Studies containing Images that match queries on their Map Annotations.
 
 
-Configuring the Categories UI
------------------------------
+Configuring the UI
+------------------
 
 **omero.web.gallery.category_queries:**
 To enable the Categories UI, you must set ``omero.web.gallery.category_queries``.
@@ -181,16 +137,6 @@ these will be shown in a dropdown menu::
 **omero.web.gallery.favicon:**
 Set a URL to a favicon to use for the browser.
 
-**omero.web.gallery.subheading_html:**
-Set some HTML to show as a sub-heading on the home page, within a <p> tag::
-
-    $ omero config set omero.web.gallery.subheading_html "This is an image gallery using <b>OMERO</b>."
-
-**omero.web.gallery.footer_html:**
-Set some HTML to show as a footer on each page::
-
-    $ omero config set omero.web.gallery.footer_html "<a href='https://blog.openmicroscopy.org/'>Blog</a>"
-
 **omero.web.gallery.study_short_name:**
 This specifies a short name for Screen or Project to show above the study Image
 in the categories or search page, instead of the default 'Project: 123'.
@@ -211,6 +157,7 @@ like: ``idr0001-graml-sysgro/screenA``::
 Release process
 ---------------
 
+- occasionally update `totalImages` and other fallback counts in loadStudyStats()
 - review and update the [CHANGELOG](https://github.com/ome/omero-gallery/blob/master/CHANGELOG.md)
 - run ``bumpversion release`` to remove the dev suffix and create a signed tag
 - run ``bumpversion --no-tag patch`` to bump the version to the next dev suffix
@@ -220,9 +167,9 @@ Release process
 License
 -------
 
-OMERO.gallery is released under the AGPL.
+`idr_gallery`` is released under the AGPL.
 
 Copyright
 ---------
 
-2016-2021, The Open Microscopy Environment
+2016-2022, The Open Microscopy Environment

idr_gallery/__init__.py

@@ -0,0 +1 @@
+default_app_config = 'idr_gallery.apps.GalleryAppConfig'

omero_gallery/apps.py → idr_gallery/apps.py

@@ -3,7 +3,7 @@
 #
 #
 #
-# Copyright (c) 2016 University of Dundee.
+# Copyright (c) 2016-2022 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
@@ -28,5 +28,5 @@
 
 
 class GalleryAppConfig(AppConfig):
-    name = "omero_gallery"
-    label = "gallery"
+    name = "idr_gallery"
+    label = "idr_gallery"

idr_gallery/data/background_images.py

@@ -0,0 +1,120 @@
+
+IDR_IMAGES = [
+    {
+        "src": "webclient/render_image/13965767/294/0/",
+        "title": "idr0124 Esteban: Heart morphogenesis",
+        "image_id": 13965767,
+        "thumbnail": "data:image/jpeg;base64,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"
+    },
+    {
+        "light": True,
+        "src": "webgateway/render_image_region/13461816/0/0/?tile=3,2,4,1024,512",
+        "title": "idr0096 Tratwal: Marrowquant",
+        "image_id": 13461816,
+    },
+    {
+        "src": "webgateway/render_image_region/9846152/45/0/?tile=4,0,0,1024,512",
+        "title": "idr0048 Abdeladim: Chroms",
+        "image_id": 9846152,
+    },
+    {
+        "light": True,
+        "src": "webgateway/render_image_region/13383922/0/0/?region=412,1224,1536,1024",
+        "title": "idr0043 Uhlen: Human Protein Atlas",
+        "image_id": 13383922,
+    },
+    {
+        "src": "webclient/render_image/4990991/0/0/?c=1|144:2250$0000FF,-2|972:2528$FFFFFF,3|126:3456$FF0000,4|131:2749$00FF00",
+        "title": "idr0050 Springer: Cyto-skeletal systems",
+        "image_id": 4990991,
+    },
+    {
+        "src": "webgateway/render_image/9846154/268/0/?region=1024,0,2048,1024&c=1|4283:12901$FF00FF,2|1278:8356$FFFF00",
+        "title": "idr0085 Walsh: MF-HREM",
+        "image_id": 9846154,
+    },
+    {
+        "src": "webclient/render_image/9753804/0/0/",
+        "title": "idr0056 Stojic: Long noncoding RNA",
+        "image_id": 9753804,
+    },
+    {
+        "src": "webgateway/render_image/9836841/0/0/",
+        "title": "idr0077 Valuchova: Flower lightsheet",
+        "image_id": 9836841,
+    },
+]
+
+CELL_IMAGES = [
+    {
+        "src": "webgateway/render_image/13417268/34/0/?c=1|5000:13880$FF0000,2|10353:50528$00FF00,3|14416:36737$0000FF",
+        "title": "idr0107 Morgan: HEI10",
+        "image_id": 13417268,
+    },
+    {
+        "src": "webgateway/render_image/12570400/0/0/?c=1|91:1391$fire.lut",
+        "title": "idr0093 Mueller: Genome-wide siRNA screen",
+        "image_id": 12570400,
+    },
+    {
+        "src": "webclient/render_image/4991918/0/0/?c=1|28:178$00FF00,3|22:110$FF0000",
+        "title": "idr0050 Springer: Cyto-skeletal systems",
+        "image_id": 4991918,
+    },
+    {
+        "light": True,
+        "src": "webgateway/render_image/9846137/92/0/?c=1|85:153$hilo.lut&m=c",
+        "title": "idr0086 Miron: Chromatin micrographs",
+        "image_id": 9846137,
+    },
+    {
+        "src": "webgateway/render_image/3005394/0/0/",
+        "title": "idr0028 Pascual-Vargas: Rho GTPases",
+        "image_id": 3005394,
+    },
+    {
+        "src": "webclient/render_image/9753804/0/0/",
+        "title": "idr0056 Stojic: Long noncoding RNA",
+        "image_id": 9753804,
+    },
+    {
+        "src": "webclient/render_image/3231645/0/0/?c=1|464:8509$FF0000,2|518:21105$00FF00,3|519:19845$0000FF",
+        "title": "idr0033 Rohban: Cell painting",
+        "image_id": 3231645,
+    },
+]
+
+TISSUE_IMAGES = [
+    {
+        "light": True,
+        "src": "webgateway/render_image_region/13461816/0/0/?tile=3,2,4,1024,512",
+        "title": "idr0096 Tratwal: Marrowquant",
+        "image_id": 13461816,
+    },
+    {
+        "src": "webgateway/render_image_region/8343616/0/0/?region=2048,6072,2024,1024&c=1|0:105$red_hot.lut&m=c",
+        "title": "idr0066 Voigt: Meso SPIM",
+        "image_id": 8343616,
+    },
+    {
+        "src": "webgateway/render_image_region/9846152/45/0/?tile=4,0,0,1024,512",
+        "title": "idr0048 Abdeladim: Chroms",
+        "image_id": 9846152,
+    },
+    {
+        "light": True,
+        "src": "webgateway/render_image_region/13383922/0/0/?region=412,1224,1536,1024",
+        "title": "idr0043 Uhlen: Human Protein Atlas",
+        "image_id": 13383922,
+    },
+    {
+        "src": "webgateway/render_image/9846154/268/0/?region=1024,0,2048,1024&c=1|4283:12901$FF00FF,2|1278:8356$FFFF00",
+        "title": "idr0085 Walsh: MF-HREM",
+        "image_id": 9846154,
+    },
+    {
+        "src": "webgateway/render_image/9836841/0/0/",
+        "title": "idr0077 Valuchova: Flower lightsheet",
+        "image_id": 9836841,
+    }
+]

idr_gallery/data/tabs.py

@@ -0,0 +1,34 @@
+TABS = [
+    {
+        "title": "Exploring IDR",
+        "text": "",
+        "videos": [
+            {
+                "id": "N9Den172mHo",
+                "title": "From publication to IDR",
+                "text": "Find a specific IDR study from a publication. View images and Regions of Interest (ROIs) in IDR. Explore study metadata.",
+            },
+            {
+                "id": "gjVZut7fL4E",
+                "title": "From gene to phenotypes",
+                "text": "Query images by gene. Explore retrieved images and metadata, including associated phenotypes. View images in context of a plate.",
+            },
+            {
+                "id": "rG-qAHZl-p0",
+                "title": "From compound to analytics",
+                "text": "Query images by compound. Find SARS-CoV-2 dataset. Explore images in relation to analytical data submitted by authors.",
+            },
+        ],
+    },
+    {
+        "title": "Analyze Data",
+        "text": "<p>The IDR server is built with <a target='_blank' href='https://www.openmicroscopy.org/omero/'>OMERO</a>, allowing access to all image data and metadata via an open API in Python, R, Java, MATLAB and REST/JSON. See the <a target='_blank' href='https://omero-guides.readthedocs.io/en/latest/api_usage.html'>OMERO API guide</a> for more information.</p><p>For examples of analysis tools working with OMERO to access and analyze data, see the <a target='_blank' href='https://omero-guides.readthedocs.io/en/latest/external_tools.html'>analysis tools guide</a>.</p>",
+        "videos": [
+            {
+                "id": "2qeJbudXnp4",
+                "title": "Compound analysis: SARS-CoV-2",
+                "text": "Build analysis environment. Access metadata and images. Calculate IC50 and download. Explore dose-response curves.",
+            }
+        ],
+    },
+]