Commit 7fb79668 authored by Boris A. Burkov's avatar Boris A. Burkov
Browse files

http://rnacentral -> https://rnacentral in docs, comments and hard-coded strings everywhere.

parent ca8e04b9
......@@ -6,7 +6,7 @@ install:
- "pip install requests selenium"
# run tests
script:
- travis_wait python rnacentral/portal/tests/selenium_tests.py --base_url=http://rnacentral.org --driver=phantomjs
- travis_wait python rnacentral/portal/tests/selenium_tests.py --base_url=https://rnacentral.org --driver=phantomjs
# define branches
branches:
only:
......
......@@ -4,7 +4,7 @@
## About
RNAcentral is an open public resource that offers integrated access to a comprehensive and up-to-date set of ncRNA sequences. For more information, please visit http://rnacentral.org/about-us.
RNAcentral is an open public resource that offers integrated access to a comprehensive and up-to-date set of ncRNA sequences. For more information, please visit https://rnacentral.org/about-us.
The development of RNAcentral is coordinated by the
[European Bioinformatics Institute](http://www.ebi.ac.uk) and is funded by the
......@@ -125,7 +125,7 @@ py.test portal/tests/description_tests.py
## Feedback
Feel free to give feedback using [GitHub issues](https://github.com/RNAcentral/rnacentral-webcode/issues)
or get in touch using the [Contact form](http://rnacentral.org/contact) on our website.
or get in touch using the [Contact form](https://rnacentral.org/contact) on our website.
## Technology overview
......@@ -157,7 +157,7 @@ or get in touch using the [Contact form](http://rnacentral.org/contact) on our w
### Testing
* [Selenium](http://www.seleniumhq.org/)
* [PhantomJS](http://phantomjs.org/)
* [Jenkins](http://rnacentral.org)
* [Jenkins](https://rnacentral.org)
* [BrowserStack](http://browserstack.com)
### Other
......
......@@ -32,7 +32,7 @@ class ExportSearchResultsTestCase(unittest.TestCase):
python export_results_tests.py
# test an RNAcentral instance
python export_results_tests.py --base_url http://test.rnacentral.org/
python export_results_tests.py --base_url https://test.rnacentral.org/
"""
base_url = ''
......
......@@ -90,7 +90,7 @@ def export_search_results(query, _format, hits):
# omit opening and closing square brackets for easy concatenation
output = output[1:-1]
# make relative urls absolute
output = output.replace('"/api/v1/', '"http://rnacentral.org/api/v1/')
output = output.replace('"/api/v1/', '"https://rnacentral.org/api/v1/')
return output
def check_ssi_file():
......
......@@ -194,7 +194,7 @@ def slack(message):
requests.post(slack_hook, json.dumps({'text': message}), headers=headers)
def deploy_locally(git_branch=None, restart_url='http://rnacentral.org', quick=False):
def deploy_locally(git_branch=None, restart_url='https://rnacentral.org', quick=False):
"""
Run deployment locally.
"""
......@@ -211,10 +211,10 @@ def deploy_locally(git_branch=None, restart_url='http://rnacentral.org', quick=F
with env.cd(settings.PROJECT_PATH):
git_branch = env.run('git rev-parse --abbrev-ref HEAD', capture=True) # env.run == local, takes capture arg
slack("Deployed '%s' at ves-hx-a4: <http://test.rnacentral.org|test.rnacentral.org>" % git_branch)
slack("Deployed '%s' at ves-hx-a4: <https://test.rnacentral.org|test.rnacentral.org>" % git_branch)
def deploy_remotely(git_branch=None, restart_url='http://rnacentral.org', quick=False):
def deploy_remotely(git_branch=None, restart_url='https://rnacentral.org', quick=False):
"""
Run deployment remotely.
"""
......@@ -230,10 +230,10 @@ def deploy_remotely(git_branch=None, restart_url='http://rnacentral.org', quick=
if not git_branch:
with env.cd(settings.PROJECT_PATH):
git_branch = env.run('git rev-parse --abbrev-ref HEAD')
slack("Deployed '%s' at %s: <http://rnacentral.org|rnacentral.org>" % (git_branch, env.host))
slack("Deployed '%s' at %s: <https://rnacentral.org|rnacentral.org>" % (git_branch, env.host))
def deploy(git_branch=None, restart_url='http://rnacentral.org', quick=False):
def deploy(git_branch=None, restart_url='https://rnacentral.org', quick=False):
"""
Deployment function wrapper that launches local or remote deployment
based on the environment.
......
......@@ -22,7 +22,7 @@ limitations under the License.
<meta name="twitter:site" content="@RNAcentral">
<meta name="twitter:creator" content="@RNAcentral">
<meta name="twitter:title" content="RNAcentral">
<meta name="twitter:image" content="http://rnacentral.org{% static "img/logo/rnacentral-logo.png" %}">
<meta name="twitter:image" content="https://rnacentral.org{% static "img/logo/rnacentral-logo.png" %}">
<meta name="robots" content="noindex">
{% endblock meta_tags %}
......
......@@ -18,7 +18,7 @@ Usage:
python tests.py
# test an RNAcentral instance
python tests.py --base_url http://test.rnacentral.org/
python tests.py --base_url https://test.rnacentral.org/
"""
from __future__ import print_function
......
......@@ -177,7 +177,7 @@ class Command(BaseCommand):
# cause domain name for sitemaps is taken from django.contrib.sites,
# but they should exist
request.META['SERVER_NAME'] = "rnacentral.org"
request.META['SERVER_PORT'] = "80"
request.META['SERVER_PORT'] = "443"
request.META['REQUEST_METHOD'] = 'GET'
request.method = 'GET'
......
......@@ -213,8 +213,8 @@ class FtpBase(object):
are compressed with Gzip. Small uncompressed example files are also provided.
Each folder contains a readme file with data description.
RNAcentral is available online at http://rnacentral.org.
For more ways of downloading the data go to http://rnacentral.org/downloads.
RNAcentral is available online at https://rnacentral.org.
For more ways of downloading the data go to https://rnacentral.org/downloads.
"""
filename = self.get_output_filename('release_notes_template.txt')
if os.path.exists(filename):
......
......@@ -178,7 +178,7 @@ class TrackDb(HubBase):
self.genome = genome
self.html = html
self.bigBed = bigBed
self.base_url = 'http://rnacentral.org'
self.base_url = 'https://rnacentral.org'
def get_track_db_path(self, filename):
"""
......
......@@ -174,8 +174,8 @@ angular.module("genomeBrowser").factory('GenoverseUtils', ['$filter', function($
}
return {
title: '<a target=_blank href="http://rnacentral.org/rna/' + feature.external_name + '/' + feature.taxid.toString() +'">'+ feature.label + '</a>',
"RNAcentral id": '<a target=_blank href="http://rnacentral.org/rna/' + feature.external_name + '/' + feature.taxid.toString() +'">' + feature.external_name + '</a>',
title: '<a target=_blank href="https://rnacentral.org/rna/' + feature.external_name + '/' + feature.taxid.toString() +'">'+ feature.label + '</a>',
"RNAcentral id": '<a target=_blank href="https://rnacentral.org/rna/' + feature.external_name + '/' + feature.taxid.toString() +'">' + feature.external_name + '</a>',
"Description": feature.description || "",
"RNA type": feature.biotype,
"Feature type": feature.feature_type,
......
......@@ -25,7 +25,7 @@ limitations under the License.
<meta name="twitter:site" content="@RNAcentral">
<meta name="twitter:creator" content="@RNAcentral">
<meta name="twitter:title" content="RNAcentral">
<meta name="twitter:image" content="http://rnacentral.org{% static "img/logo/rnacentral-logo.png" %}">
<meta name="twitter:image" content="https://rnacentral.org{% static "img/logo/rnacentral-logo.png" %}">
{% endblock meta_tags %}
<base href="/"/>
......
......@@ -16,24 +16,24 @@ On this page:
Databases [integrated in RNAcentral](/expert-databases) can display
an **RNAcentral Expert Database badge**:
<a href="http://rnacentral.org" style="text-decoration: none;">
<a href="https://rnacentral.org" style="text-decoration: none;">
<img src="/static/img/logo/rnacentral-expert-database.svg"
style="width: 140px;">
</a>
<a class="btn btn-default" style="margin-left: 20px;" target="_blank" href="http://rnacentral.org/static/img/logo/rnacentral-expert-database.svg">Download (svg)</a>
<a class="btn btn-default" style="margin-left: 20px;" target="_blank" href="https://rnacentral.org/static/img/logo/rnacentral-expert-database.svg">Download (svg)</a>
Example code:
```
<a href="http://rnacentral.org">
<img src="http://rnacentral.org/static/img/logo/rnacentral-expert-database.svg" style="width: 140px">
<a href="https://rnacentral.org">
<img src="https://rnacentral.org/static/img/logo/rnacentral-expert-database.svg" style="width: 140px">
</a>
```
The badge should link to the [RNAcentral homepage](http://rnacentral.org)
The badge should link to the [RNAcentral homepage](https://rnacentral.org)
or to the **landing page** of the member database within RNAcentral,
such as [http://rnacentral.org/expert-database/flybase](http://rnacentral.org/expert-database/flybase) or
[http://rnacentral.org/expert-database/gtrnadb](http://rnacentral.org/expert-database/gtrnadb).
such as [https://rnacentral.org/expert-database/flybase](https://rnacentral.org/expert-database/flybase) or
[https://rnacentral.org/expert-database/gtrnadb](https://rnacentral.org/expert-database/gtrnadb).
---
......@@ -43,7 +43,7 @@ such as [http://rnacentral.org/expert-database/flybase](http://rnacentral.org/ex
Please use the following format to link to RNAcentral sequences:
`http://rnacentral.org/rna/<RNAcentral identifier>/<NCBI taxonomy identifier>`
`https://rnacentral.org/rna/<RNAcentral identifier>/<NCBI taxonomy identifier>`
The URL includes
[NCBI taxonomy identifiers](https://www.ncbi.nlm.nih.gov/taxonomy), for example
......@@ -68,8 +68,8 @@ Example code:
```
<p>
<img src="http://rnacentral.org/static/img/logo/rnacentral-logo.png" style="width: 16px; height: 16px; vertical-align: middle;">
<a href="http://rnacentral.org/rna/URS000075A546/9606">URS000075A546/9606</a>
<img src="https://rnacentral.org/static/img/logo/rnacentral-logo.png" style="width: 16px; height: 16px; vertical-align: middle;">
<a href="https://rnacentral.org/rna/URS000075A546/9606">URS000075A546/9606</a>
</p>
```
......@@ -96,7 +96,7 @@ please use the mapping files found in FTP archive:
You can link to a genome location of interest within the RNAcentral genome browser using links like this:
`http://rnacentral.org/genome-browser?species=<species>&chromosome=<chromosome>&start=<start>&end=<end>`
`https://rnacentral.org/genome-browser?species=<species>&chromosome=<chromosome>&start=<start>&end=<end>`
where:
......@@ -108,15 +108,15 @@ Example:
<p>
<img src="/static/img/logo/rnacentral-logo.png" style="width: 16px; height: 16px; vertical-align: middle;">
<a href="http://rnacentral.org/genome-browser?species=homo_sapiens&chromosome=X&start=73819307&end=73856333">Human XIST gene</a>
<a href="https://rnacentral.org/genome-browser?species=homo_sapiens&chromosome=X&start=73819307&end=73856333">Human XIST gene</a>
</p>
Example code:
```
<p>
<img src="http://rnacentral.org/static/img/logo/rnacentral-logo.png" style="width: 16px; height: 16px; vertical-align: middle;">
<a href="http://rnacentral.org/genome-browser?species=homo_sapiens&chromosome=X&start=73819307&end=73856333">Human XIST gene</a>
<img src="https://rnacentral.org/static/img/logo/rnacentral-logo.png" style="width: 16px; height: 16px; vertical-align: middle;">
<a href="https://rnacentral.org/genome-browser?species=homo_sapiens&chromosome=X&start=73819307&end=73856333">Human XIST gene</a>
</p>
```
......@@ -128,12 +128,12 @@ Example code:
Here are RNAcentral logo icons in different resolutions:
* <a target="_blank" href="http://rnacentral.org/static/img/logo/rnacentral-logo-16x16.png">16x16</a>
* <a target="_blank" href="http://rnacentral.org/static/img/logo/rnacentral-logo-24x24.png">24x24</a>
* <a target="_blank" href="http://rnacentral.org/static/img/logo/rnacentral-logo-32x32.png">32x32</a>
* <a target="_blank" href="http://rnacentral.org/static/img/logo/rnacentral-logo-64x64.png">64x64</a>
* <a target="_blank" href="http://rnacentral.org/static/img/logo/rnacentral-logo-128x128.png">128x128</a>
* <a target="_blank" href="/static/img/logo/rnacentral-logo.png">530x530</a>
* <a target="_blank" href="https://rnacentral.org/static/img/logo/rnacentral-logo-16x16.png">16x16</a>
* <a target="_blank" href="https://rnacentral.org/static/img/logo/rnacentral-logo-24x24.png">24x24</a>
* <a target="_blank" href="https://rnacentral.org/static/img/logo/rnacentral-logo-32x32.png">32x32</a>
* <a target="_blank" href="https://rnacentral.org/static/img/logo/rnacentral-logo-64x64.png">64x64</a>
* <a target="_blank" href="https://rnacentral.org/static/img/logo/rnacentral-logo-128x128.png">128x128</a>
* <a target="_blank" href="https://rnacentral.org/static/img/logo/rnacentral-logo.png">530x530</a>
---
......
......@@ -310,10 +310,10 @@ $(document).ready(function() {
{
"@context": "http://schema.org",
"@type": "WebSite",
"url": "http://rnacentral.org/",
"url": "https://rnacentral.org/",
"potentialAction": {
"@type": "SearchAction",
"target": "http://rnacentral.org/search?q={search_term_string}",
"target": "https://rnacentral.org/search?q={search_term_string}",
"query-input": "required name=search_term_string"
}
}
......
......@@ -33,10 +33,10 @@ limitations under the License.
python selenium_tests.py
# test an RNAcentral instance
python selenium_tests.py --base_url http://test.rnacentral.org/
python selenium_tests.py --base_url https://test.rnacentral.org/
# test an RNAcentral instance using PhantomJS
python selenium_tests.py --base_url http://test.rnacentral.org/ --driver=phantomjs
python selenium_tests.py --base_url https://test.rnacentral.org/ --driver=phantomjs
# test a specific method in a specific test case
python selenium_tests.py RNAcentralTest.test_url_changed_on_input_changed --driver=phantomjs
......
......@@ -49,10 +49,10 @@ misc_RNA: SO:0000673
isn't a good SO term for this at all. The best I can do is assign to it the
'transcript' type. This is kind of wrong. These sequences are sometimes a
processed transcript, that has been incorrectly assigned 'misc_RNA':
http://rnacentral.org/rna/URS00004A2461/9606 (is a Y_RNA). We are probably
https://rnacentral.org/rna/URS00004A2461/9606 (is a Y_RNA). We are probably
best of trying to avoid the misc_RNA label as much as possible. However,
there are times times it is truly unclear:
http://rnacentral.org/rna/URS0000256D95/9606. Some minor browsing does show
https://rnacentral.org/rna/URS0000256D95/9606. Some minor browsing does show
at least a couple sequences which are transcripts so hopefully this isn't
too wrong. Overall we should just avoid sequences that have this term, it's
not very informative
......
......@@ -3,4 +3,4 @@ Disallow: /sequence-search/job-status
Disallow: /sequence-search/cancel-job
Disallow: /sequence-search/submit-query
Sitemap: http://rnacentral.org/sitemap.xml
Sitemap: https://rnacentral.org/sitemap.xml
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