Idr prototype

omero_gallery/gallery_settings.py

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+#!/usr/bin/env python
+# -*- coding: utf-8 -*-
+
+# Copyright (C) 2019 University of Dundee & Open Microscopy Environment.
+# All rights reserved.
+#
+# 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/>.
+
+"""Settings for the OMERO.gallery app."""
+
+import sys
+from omeroweb.settings import process_custom_settings, report_settings
+import json
+
+# load settings
+GALLERY_SETTINGS_MAPPING = {
+
+    "omero.web.gallery.base_url":
+        ["BASE_URL",
+         'https://idr.openmicroscopy.org',  # TODO: - should be None
+         str,
+         ("Base URL to use for JSON AJAX requests."
+          "This allows data to be loaded from another OMERO server."
+          "The default behaviour is to use the current server.")],
+
+    "omero.web.gallery.category_queries":
+        ["CATEGORY_QUERIES",
+         ('['
+          '{"label": "Time-lapse", "query": "Study Type:time OR Study Type:5D'
+          ' OR Study Type:3D-tracking"},'
+          '{"label": "Light sheet", "query": "Study Type:light sheet"},'
+          '{"label": "Protein localization", "query": "Study Type:protein'
+          ' localization"},'
+          '{"label": "Histology", "query": "Study Type:histology"},'
+          '{"label": "Yeast", "query": "Organism:Saccharomyces cerevisiae OR'
+          ' Organism:Schizosaccharomyces pombe"},'
+          '{"label": "Human Cell Screen", "query": "Organism:Homo sapiens AND'
+          ' Study Type:high content screen"}'
+          ']'),    # TODO: - should be []
+         json.loads,
+         ("")],
+
+}
+
+process_custom_settings(sys.modules[__name__], 'GALLERY_SETTINGS_MAPPING')
+report_settings(sys.modules[__name__])

omero_gallery/static/gallery/idr/constants.js

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+const THUMB_IDS = {'project-701': 5025553, 'project-504': 4495405, 'project-754': 5514116, 'project-753': 5514054, 'project-752': 5514379,
+           'project-552': 4007821, 'project-505': 4991000, 'project-503': 4496813, 'project-405': 3509516, 'project-502': 4007804,
+           'project-501': 3899001, 'project-402': 3429220, 'project-404': 3430746, 'project-401': 3490890, 'project-353': 3414088,
+           'project-352': 3414075, 'project-351': 3414020, 'screen-1654': 3002517, 'screen-1653': 2959817, 'screen-1901': 3261920,
+           'screen-2001': 3414101, 'screen-1952': 1895788, 'project-201': 3125701, 'screen-1651': 2868079, 'project-151': 2858200,
+           'screen-1652': 2892586, 'screen-1801': 3126552, 'screen-1751': 3191232, 'project-301': 3261651, 'screen-1851': 3260452,
+           'project-52': 1885617, 'screen-2051': 4996332, 'project-51': 1884807, 'screen-1204': 1874776, 'screen-1203': 1851808,
+           'project-101': 1919065, 'screen-1151': 1674502, 'screen-1251': 2042278, 'screen-1201': 1816624, 'screen-1302': 2858452,
+           'screen-1101': 1483352, 'screen-1202': 1811248, 'screen-1603': 2857882, 'screen-1251': 2042278, 'screen-1602': 2958952,
+           'screen-1601': 2857796, 'screen-1551': 2855969, 'screen-1501': 2849751, 'screen-1351': 1921252, 'screen-803': 1313418,
+           'screen-251': 171248, 'screen-206': 106450, 'screen-154': 35446, 'screen-201': 95412, 'screen-253': 352577,
+           'screen-751': 928389, 'screen-597': 933573, 'screen-202': 692151, 'screen-51': 13852, 'screen-102':179694, 'screen-3': 1463}
+
+const FILTER_KEYS = ["Imaging Method", "Organism", "Publication Authors", "Publication Title",
+                     "Screen Technology Type", "Screen Type", "Study Type"]
+
+// We hard-code filtering, but could use e.g. Tags on Studies to specify Cells/Tissue
+let TISSUE_STUDIES = ['idr0018', 'idr0032', 'idr0042', 'idr0043', 'idr0054'];

omero_gallery/static/gallery/idr/idr.css

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+code {
+    background-color: transparent;
+    border: none;
+    color: #1a237e;
+    font-family: Courier, serif;
+    font-weight: normal;
+    padding: 0.125rem 0.3125rem 0.0625rem;
+    width: 200px;
+}
+
+.highlight {
+    background-color: #e8eaf6;
+    border-radius: 3px;
+    overflow-x: scroll;
+    padding: 1rem;
+}
+
+.bold {
+    color: #37474F;
+    font-weight: bold;
+}
+
+body {
+    background-color: #f4f5f9;
+    color: #455a64;
+    font-family: 'Open Sans', sans-serif;
+}
+
+h1,h2,h3,h4,h5,h6 {
+    color: #1976d2;
+    font-family: 'Nunito', sans-serif;
+    font-weight: bold;
+}
+
+h1 {
+    font-size: 1.5rem; }
+
+h2 {
+  font-size: 1.25rem; }
+
+h3 {
+  font-size: 1.0625em; }
+
+h4 {
+  font-size: 1.0312rem;
+  margin-top: 4rem;
+}
+
+h5 {
+  font-size: 1rem; }
+
+h6 {
+  font-size: 0.875rem; }
+
+hr {
+    border-style: dashed;
+}
+
+a.button {
+    background-color: #ff9800;
+    font-weight: bold;
+}
+
+a.button:hover {
+    background-color: #ffc107;
+}
+
+a {
+    color: #3949ab;
+    font-weight: bold;
+}
+
+.logo { max-width: 150px; }
+.logo.centered { margin: 20px auto; }
+.logo.sidebar { margin: 20px 0 20px 15px; }
+
+.menu.documentation {
+    background: transparent none repeat scroll 0 0;
+    margin-top: 0.5rem;
+    padding-bottom: 1rem;
+    padding-top: 1rem;
+}
+
+.content {
+    background-color: #fff;
+    border-left: 1px solid #cfd8dc;
+    margin-bottom: -50px;  
+    padding-bottom: 50px;
+}   
+
+.marketing-hero {
+    background-color: #e8eaf6;
+    background-image: url('../img/bg/11001_Well_A07_Field_1.jpg');
+    background-position: top left;
+    padding: 80px 10px 80px;
+}
+
+.marketing-hero h1, .marketing-hero h2, .marketing-hero p {
+    color: #fff;
+}
+
+.marketing-hero h1 {
+    font-size: 2rem;
+    margin-bottom: 20px;
+}
+
+.marketing-hero p > a {
+    border-bottom: 1px dashed #fefefe;
+    color: #fefefe;
+}
+
+.marketing-hero p > a:hover {
+    border-bottom: none;
+    color: #fff;
+}
+
+#page-anchor {
+    font-size: .8rem;
+    margin-top: 50px;
+    text-align: center;   
+}
+
+.callout.secondary {
+    background-color: #fff;
+    border: 1px solid #cfd8dc;
+    color: #90a4ae;
+}
+
+.centered {
+    margin: auto;
+}
+
+/* ---------- main navigation ----------*/
+.logo {
+    display: inline;
+    width: 120px;
+}
+
+.logo-hero {
+    margin-bottom: 30px;
+    width: 160px;
+}
+
+.top-bar {
+    background-color: #263238;
+    border-bottom: 1px solid #000;
+}
+
+.top-bar ul {
+    background-color: #263238;
+}
+
+.top-bar ul li {
+    vertical-align: middle;
+}
+
+.nav-secondary, .nav-secondary ul {
+    background-color: #37474f;
+    border-bottom: 1px solid #000;
+    font-size: 0.875em;
+    height: 36px;
+}
+
+.nav-secondary > .top-bar-right > .menu > li > a {
+    color: #eceff1;
+}
+
+.nav-secondary > .top-bar-right > .menu > li > a:hover {
+    color: #fff;
+}
+
+.nav-secondary > .top-bar-right > .menu > li > a i {
+    vertical-align: top;
+}
+
+#main-menu .is-dropdown-submenu {
+    border-color: #000;
+}
+#main-menu a {
+    color: #eceff1;
+    font-family: 'Montserrat', Helvetica, Roboto, Arial, sans-serif;
+    font-size: 0.8125rem;
+    text-transform: uppercase;
+}
+
+#main-menu a:hover {
+    color: #fff;
+}
+
+#main-menu .dropdown.menu > li.is-dropdown-submenu-parent > a::after {
+    border-color: #eceff1 transparent transparent;
+}
+
+#version-number { 
+    margin-right: 5px;
+    width: 50px;
+}
+.version-number {
+    font-size: 11px;
+    font-weight: bold;
+}