12 |
13 |
23 |
24 | {% endblock %}
25 |
--------------------------------------------------------------------------------
/omeroweb/feedback/templates/base_error.html:
--------------------------------------------------------------------------------
1 | {% extends "webgateway/core_html.html" %}
2 | {% load i18n %}
3 |
4 | {% block link %}
5 | {{ block.super }}
6 |
7 | {% endblock %}
8 |
9 | {% block title %}
10 | {% trans "OMERO.web - support" %}
11 | {% endblock %}
12 |
13 | {% block body %}
14 | No Processor Available
14 | 15 | 16 |The script service cannot find a processor to run this script ID: {{ scriptId }}. You should contact your System Administrator.
17 | 18 |
19 | Close Window
20 |
21 |
22 |
15 |
20 |
21 |
22 | {% endblock %}
23 |
24 |
--------------------------------------------------------------------------------
/omeroweb/feedback/templates/error.html:
--------------------------------------------------------------------------------
1 | {% extends "webgateway/core_html.html" %}
2 | {% load i18n %}
3 |
4 | {% block link %}
5 | {{ block.super }}
6 |
7 | {% endblock %}
8 |
9 | {% block title %}
10 | {% trans "Web - Internal Error" %}
11 | {% endblock %}
12 |
13 | {% block body %}
14 |
15 | 16 | {% trans "Go back to" %} {% trans "OMERO.web" %} 17 |
18 | {% block content %}{% endblock %} 19 |
16 |
22 | {% endblock %}
23 |
24 |
25 | {% endblock %}
26 |
--------------------------------------------------------------------------------
/omeroweb/feedback/templates/thanks.html:
--------------------------------------------------------------------------------
1 | {% extends "webgateway/core_html.html" %}
2 | {% load i18n %}
3 |
4 | {% block link %}
5 | {{ block.super }}
6 |
7 | {% endblock %}
8 |
9 | {% block title %}
10 | {% trans "OMERO.web - support" %}
11 | {% endblock %}
12 |
13 | {% block body %}
14 | 17 | {% trans "Go back to" %}: {% trans "OMERO.web" %} 18 |
19 | 20 | {% block content %} 21 |{{ error }}
15 |
20 |
21 |
22 |
23 | {% endblock %}
24 |
25 |
--------------------------------------------------------------------------------
/omeroweb/feedback/templates/500-nosubmit.html:
--------------------------------------------------------------------------------
1 | {% extends "base_error.html" %}
2 | {% load i18n %}
3 |
4 | {% block content %}
5 | 16 | {% trans "Close" %} 17 |
18 | {% block content %}{% trans "Thank you for your feedback." %}
{% endblock %} 19 |
6 |
16 | {% endblock %}
17 |
--------------------------------------------------------------------------------
/.github/workflows/publish_pypi.yml:
--------------------------------------------------------------------------------
1 | ---
2 | name: PyPI
3 | on: push
4 |
5 | jobs:
6 | build-n-publish:
7 | name: Build and publish Python distribution to PyPI
8 | runs-on: ubuntu-latest
9 | steps:
10 | - uses: actions/checkout@v4
11 | - uses: actions/setup-python@v5
12 | with:
13 | python-version: '3.10'
14 | - name: Build a binary wheel and a source tarball
15 | run: |
16 | python -mpip install build
17 | python -m build
18 | - name: Publish distribution to PyPI
19 | if: startsWith(github.ref, 'refs/tags')
20 | uses: pypa/gh-action-pypi-publish@release/v1
21 | with:
22 | password: ${{ secrets.PYPI_PASSWORD }}
23 |
--------------------------------------------------------------------------------
/omeroweb/webgateway/static/webgateway/css/ome.iehacks.css:
--------------------------------------------------------------------------------
1 | /**
2 | * weblitz_viewport - style definitions
3 | *
4 | * Copyright (c) 2007, 2008, 2009 Glencoe Software, Inc. All rights reserved.
5 | *
6 | * This software is distributed under the terms described by the LICENCE file
7 | * you can find at the root of the distribution bundle, which states you are
8 | * free to use it only for non commercial purposes.
9 | * If the file is missing please request a copy by contacting
10 | * jason@glencoesoftware.com.
11 | *
12 | * Author: Carlos Neves {% trans "Server Error." %} (500)
7 | 8 |{% trans "The server encountered an internal error and was unable to complete your request. Please contact your system administrator with the error message below." %}
9 | 10 | {% if error %}- {{ error }}
15 |
26 |
27 | {% endblock %}
28 |
--------------------------------------------------------------------------------
/.github/workflows/tox.yml:
--------------------------------------------------------------------------------
1 | ---
2 | name: Tox
3 | on:
4 | push:
5 | pull_request:
6 |
7 | jobs:
8 | test:
9 | name: Run tox tests
10 | strategy:
11 | fail-fast: false
12 | matrix:
13 | python-version:
14 | - '3.10'
15 | - '3.11'
16 | - '3.12'
17 | runs-on: ubuntu-22.04
18 | steps:
19 | - uses: actions/checkout@v4
20 | - uses: actions/setup-python@v5
21 | with:
22 | python-version: ${{ matrix.python-version }}
23 | - name: Install dependencies
24 | run: python -mpip install --upgrade wheel pytest tox setuptools
25 | - name: Get tox target
26 | id: toxtarget
27 | run: |
28 | py=$(echo ${{ matrix.python-version }} | tr -d .)
29 | echo "py=$py" >> $GITHUB_OUTPUT
30 | - name: Run tests
31 | run: tox -e py${{ steps.toxtarget.outputs.py }}
32 |
--------------------------------------------------------------------------------
/omeroweb/api/__init__.py:
--------------------------------------------------------------------------------
1 | #!/usr/bin/env python
2 | # -*- coding: utf-8 -*-
3 |
4 | # Copyright (C) 2016 University of Dundee & Open Microscopy Environment.
5 | # All rights reserved.
6 | #
7 | # This program is free software: you can redistribute it and/or modify
8 | # it under the terms of the GNU Affero General Public License as
9 | # published by the Free Software Foundation, either version 3 of the
10 | # License, or (at your option) any later version.
11 | #
12 | # This program is distributed in the hope that it will be useful,
13 | # but WITHOUT ANY WARRANTY; without even the implied warranty of
14 | # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
15 | # GNU Affero General Public License for more details.
16 | #
17 | # You should have received a copy of the GNU Affero General Public License
18 | # along with this program. If not, see 16 | {% trans "Close" %} 17 |
18 | {% block content %} 19 |
20 |
24 |
25 | Feedback is disabled on this server
21 |Please contact your system administrator or the Open Microscopy Environment
22 | {% endblock %} 23 |-
2 |
3 |
-
4 |
6 | title="Click to add rating" 7 | <% } else { %> 8 | title="You don't have permissions to add rating" 9 | <% } %> 10 | <% if (average) { %> 11 | src="<%= static %>image/rating<%= average %>.png" 12 | <% } else { %> 13 | src="<%= static %>image/rating0.png" 14 | <% } %> 15 | /> 16 | 17 | <% if (canAnnotate) { %> 18 | X 19 | <% } %> 20 |
21 |
style="display:none"<% } %> >
23 | (avg:
24 | <%= average %>
25 | / <%= count %>
26 | votes)
27 |
--------------------------------------------------------------------------------
/omeroweb/webgateway/templates/webgateway/base/includes/shortcut_icon.html:
--------------------------------------------------------------------------------
1 | {% comment %}
2 |
19 | {% endcomment %}
20 |
21 |
22 |
23 |
--------------------------------------------------------------------------------
/omeroweb/webgateway/templates/webgateway/base/includes/css_link_body.html:
--------------------------------------------------------------------------------
1 | {% comment %}
2 |
19 | {% endcomment %}
20 |
21 |
--------------------------------------------------------------------------------
/omeroweb/webgateway/templates/webgateway/base/includes/script_src_popup.html:
--------------------------------------------------------------------------------
1 | {% comment %}
2 |
19 | {% endcomment %}
20 |
21 |
--------------------------------------------------------------------------------
/omeroweb/webgateway/templates/webgateway/base/includes/post_form.html:
--------------------------------------------------------------------------------
1 | {% load i18n %}
2 | {% comment %}
3 |
20 | {% endcomment %}
21 |
22 |
25 |
--------------------------------------------------------------------------------
/omeroweb/webclient/templates/webclient/base/includes/logout.html:
--------------------------------------------------------------------------------
1 | {% load i18n %}
2 | {% comment %}
3 |
20 | {% endcomment %}
21 |
22 |
25 |
--------------------------------------------------------------------------------
/omeroweb/webgateway/templates/webgateway/base/includes/script_src_jquery.html:
--------------------------------------------------------------------------------
1 | {% comment %}
2 |
19 | {% endcomment %}
20 |
21 |
22 |
23 |
24 |
25 |
--------------------------------------------------------------------------------
/omeroweb/webredirect/urls.py:
--------------------------------------------------------------------------------
1 | #!/usr/bin/env python
2 | # -*- coding: utf-8 -*-
3 | #
4 | #
5 | #
6 | # Copyright (c) 2008-2014 University of Dundee.
7 | #
8 | # This program is free software: you can redistribute it and/or modify
9 | # it under the terms of the GNU Affero General Public License as
10 | # published by the Free Software Foundation, either version 3 of the
11 | # License, or (at your option) any later version.
12 | #
13 | # This program is distributed in the hope that it will be useful,
14 | # but WITHOUT ANY WARRANTY; without even the implied warranty of
15 | # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
16 | # GNU Affero General Public License for more details.
17 | #
18 | # You should have received a copy of the GNU Affero General Public License
19 | # along with this program. If not, see 
{{ error }}
27 | {% else %}
28 | 
Password reset OK
29 | {% endif %}
30 |
--------------------------------------------------------------------------------
/omeroweb/webadmin/webadmin_utils.py:
--------------------------------------------------------------------------------
1 | #!/usr/bin/env python
2 | # -*- coding: utf-8 -*-
3 | import logging
4 |
5 | logger = logging.getLogger(__name__)
6 |
7 |
8 | def upgradeCheck(url):
9 | # upgrade check:
10 | # -------------
11 | # On each startup OMERO.web checks for possible server upgrades
12 | # and logs the upgrade url at the WARNING level. If you would
13 | # like to disable the checks, please set 'omero.web.upgrades_url`
14 | # to an empty string.
15 | #
16 | # For more information, see
17 | # https://docs.openmicroscopy.org/latest/omero/sysadmins/UpgradeCheck.html
18 | #
19 | try:
20 | from omero.util.upgrade_check import UpgradeCheck
21 |
22 | if url:
23 | check = UpgradeCheck("web", url=url)
24 | check.run()
25 | if check.isUpgradeNeeded():
26 | logger.warn(
27 | "Upgrade is available. Please visit"
28 | " https://downloads.openmicroscopy.org/latest/omero/.\n"
29 | )
30 | else:
31 | logger.debug("Up to date.\n")
32 | except Exception as x:
33 | logger.error("Upgrade check error: %s" % x)
34 |
--------------------------------------------------------------------------------
/omeroweb/webgateway/static/3rdparty/jquery.flot-0.8.3/LICENSE.txt:
--------------------------------------------------------------------------------
1 | Copyright (c) 2007-2014 IOLA and Ole Laursen
2 |
3 | Permission is hereby granted, free of charge, to any person
4 | obtaining a copy of this software and associated documentation
5 | files (the "Software"), to deal in the Software without
6 | restriction, including without limitation the rights to use,
7 | copy, modify, merge, publish, distribute, sublicense, and/or sell
8 | copies of the Software, and to permit persons to whom the
9 | Software is furnished to do so, subject to the following
10 | conditions:
11 |
12 | The above copyright notice and this permission notice shall be
13 | included in all copies or substantial portions of the Software.
14 |
15 | THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
16 | EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
17 | OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
18 | NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
19 | HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
20 | WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
21 | FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
22 | OTHER DEALINGS IN THE SOFTWARE.
23 |
--------------------------------------------------------------------------------
/omeroweb/webclient/templates/webclient/base/includes/logo.html:
--------------------------------------------------------------------------------
1 | {% load i18n %}
2 | {% comment %}
3 |
20 | {% endcomment %}
21 |
22 |
27 | {% if ome.logo_src %}
28 |
23 |
31 |
--------------------------------------------------------------------------------
/omeroweb/webgateway/static/webgateway/css/reset.css:
--------------------------------------------------------------------------------
1 | /* http://meyerweb.com/eric/tools/css/reset/
2 | v2.0 | 20110126
3 | License: none (public domain)
4 | */
5 |
6 | html, body, div, span, applet, object, iframe,
7 | h1, h2, h3, h4, h5, h6, p, blockquote, pre,
8 | a, abbr, acronym, address, big, cite, code,
9 | del, dfn, em, img, ins, kbd, q, s, samp,
10 | small, strike, strong, sub, sup, tt, var,
11 | b, u, i, center,
12 | dl, dt, dd, ol, ul, li,
13 | fieldset, form, label, legend,
14 | table, caption, tbody, tfoot, thead, tr, th, td,
15 | article, aside, canvas, details, embed,
16 | figure, figcaption, footer, header, hgroup,
17 | menu, nav, output, ruby, section, summary,
18 | time, mark, audio, video {
19 | margin: 0;
20 | padding: 0;
21 | border: 0;
22 | font-size: 100%;
23 | font: inherit;
24 | vertical-align: baseline;
25 | font-family: Helvetica, Arial, sans-serif;
26 | }
27 | /* HTML5 display-role reset for older browsers */
28 | article, aside, details, figcaption, figure,
29 | footer, header, hgroup, menu, nav, section {
30 | display: block;
31 | }
32 | body {
33 | line-height: 1;
34 | }
35 | ol, ul {
36 | list-style: none;
37 | }
38 | blockquote, q {
39 | quotes: none;
40 | }
41 | blockquote:before, blockquote:after,
42 | q:before, q:after {
43 | content: '';
44 | content: none;
45 | }
46 | table {
47 | border-collapse: collapse;
48 | border-spacing: 0;
49 | }
--------------------------------------------------------------------------------
/omeroweb/webclient/templates/webclient/annotations/custom_ann_tooltip.html:
--------------------------------------------------------------------------------
1 |
2 | {% comment %}
3 |
20 | {% endcomment %}
21 |
22 |
--------------------------------------------------------------------------------
/omeroweb/webclient/templates/webclient/annotations/includes/metadata_general_map.html:
--------------------------------------------------------------------------------
1 | {% comment %}
2 |
19 | {% endcomment %}
20 |
21 |
22 | 24 | {{ label|default:"Others" }} 25 | {{ annotationCounts.OtherAnnotation }} 26 |
27 | 30 |
23 |
33 |
--------------------------------------------------------------------------------
/omeroweb/webclient/templates/webclient/annotations/includes/metadata_general_table.html:
--------------------------------------------------------------------------------
1 | {% comment %}
2 |
19 | {% endcomment %}
20 |
21 |
22 | {% if manager.well or manager.image %}
23 | 24 | {{ label|default:"Key-Value Pairs" }} 25 | {{ annotationCounts.MapAnnotation }} 26 |
27 | 32 |24 | {{ label|default:"Tables" }} {{ tableCountsOnParents }} 25 |
26 | 32 | {% endif %} 33 | -------------------------------------------------------------------------------- /omeroweb/webclient/templates/webclient/base/includes/script_launch.html: -------------------------------------------------------------------------------- 1 | {% comment %} 2 | 19 | {% endcomment %} 20 | 21 | 22 |
26 |
27 |
28 |
29 |
30 |
35 |
36 | {% endblock %}
37 |
--------------------------------------------------------------------------------
/omeroweb/webclient/templates/webclient/annotations/includes/figure_scripts_menu.html:
--------------------------------------------------------------------------------
1 | {% comment %}
2 |
19 | {% endcomment %}
20 |
21 |
22 |
--------------------------------------------------------------------------------
/omeroweb/webclient/templates/webclient/scripts/list_scripts.html:
--------------------------------------------------------------------------------
1 | {% load i18n %}
2 |
3 | {% comment %}
4 |
21 | {% endcomment %}
22 |
23 | {% comment %}
24 |
27 | {% endcomment %}
28 |
29 | {% for folder in scriptMenu %}
30 |
31 |
34 | {% trans "Email Announcement Unavailable" %}
32 |This is because there are not sufficient settings configured to facilitate sending emails. Please configure OMERO web according to the documentation and restart the web server.
33 |-
33 | {% for script in folder.scripts %}
34 |
- {{ script.1 }}... 35 | {% endfor %} 36 |
8 | <% if (ann.type === 'Xml') { %>
9 |
20 |
21 |
34 | <% print(_.escape((ann.value + "").slice(0, 20))) %>...
10 | Open in new window
11 |
12 | <% } else if (ann.value != null) { %>
13 | <%- ann.value %>
14 | <% } else if (ann.type === 'List' && ann.name) { %>
15 | <%- ann.name %>
16 | <% } else { %>
17 | (No data)
18 | <% } %>
19 |
3 |
4 |
38 | <% }) %>
39 |
--------------------------------------------------------------------------------
/omeroweb/webgateway/templates/webgateway/base/includes/jquery-ui.html:
--------------------------------------------------------------------------------
1 | {% comment %}
2 |
19 | {% endcomment %}
20 |
21 |
22 |
23 |
24 |
25 |
--------------------------------------------------------------------------------
5 | 
8 |
9 |
10 |
11 | 
24 | <% } %>
25 |
26 |
28 |
29 | <% if (ann.ns || ann.description) { %>
30 |
35 | <% } %>
36 |
37 |
12 |
13 | <%- ann.owner.firstName %> <%- ann.owner.lastName %>
14 |
15 | at
16 | <% print(OME.formatDate(ann.link.date)) %>
17 |
18 |
19 | <% if (ann.permissions.canDelete) { %>
20 |
24 | <% } %>
25 |
26 | <%- ann.textValue %>
27 |