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get links to https where we can; for #2154
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@kltm
kltm committed Oct 30, 2023
1 parent 1346515 commit 785994b
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Showing 2 changed files with 38 additions and 35 deletions.
3 changes: 3 additions & 0 deletions scripts/downloads-page-gen.py
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Expand Up @@ -115,10 +115,13 @@ def main():
paint_version_id = 'paint_' + entry["id"]
if entry_hash.get(paint_version_id, False):
## ...if it does, add it to create a new full count...
LOG.info('Found paint version: ' + paint_version_id + ' (' + str(int(entry_hash[paint_version_id]["associations"])) + ') for ' + entry["id"] + ' (' + str(int(entry["associations"])) + ')')
entry["full_count"] = int(entry["associations"]) + int(entry_hash[paint_version_id]["associations"])
else:
## ...otherwise, just use the local count for the full count.
LOG.info('No paint version: ' + entry["id"])
entry["full_count"] = int(entry["associations"])
LOG.info(' Count: ' + str(entry["full_count"]))

# ## Read in all of the useful data from the metadata data sources.
# for datum in read_data:
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70 changes: 35 additions & 35 deletions scripts/downloads-page-template.html
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Expand Up @@ -17,7 +17,7 @@
<!-- <meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"> -->
<meta name="viewport" content="width=device-width, initial-scale=1.0">
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
<link rel="shortcut icon" href="http://geneontology.org/assets/go-logo-favicon.ico" type="image/vnd.microsoft.icon" />
<link rel="shortcut icon" href="https://geneontology.org/assets/go-logo-favicon.ico" type="image/vnd.microsoft.icon" />
<link rel="shortcut icon" href="logo-circle.ico">
<link rel="stylesheet" href="https://maxcdn.bootstrapcdn.com/bootstrap/4.0.0-alpha.6/css/bootstrap.min.css" integrity="sha384-rwoIResjU2yc3z8GV/NPeZWAv56rSmLldC3R/AZzGRnGxQQKnKkoFVhFQhNUwEyJ" crossorigin="anonymous">
<link rel="stylesheet" href="https://cdn.datatables.net/1.10.13/css/jquery.dataTables.min.css" crossorigin="anonymous">
Expand All @@ -37,69 +37,69 @@
<span class="navbar-toggler-icon"></span>
</button>

<a class="navbar-brand" href="http://geneontology.org/">
<img src="http://geneontology.org/assets/go-logo.large.png" height="30" class="d-inline-block align-top" alt="">
<a class="navbar-brand" href="https://geneontology.org/">
<img src="https://geneontology.org/assets/go-logo.large.png" height="30" class="d-inline-block align-top" alt="">
</a>

<div class="collapse navbar-collapse" id="navbarsExampleDefault">
<ul class="navbar-nav mr-auto">

<li class="nav-item">
<a class="nav-link" href="http://geneontology.org" id="nav01" aria-haspopup="true" aria-expanded="false">Home</a>
<a class="nav-link" href="https://geneontology.org" id="nav01" aria-haspopup="true" aria-expanded="false">Home</a>
</li>

<li class="nav-item dropdown">
<a class="nav-link dropdown-toggle" href="http://geneontology.org/docs/introduction-to-go" id="nav02" data-toggle="dropdown" aria-haspopup="true" aria-expanded="false">About</a>
<a class="nav-link dropdown-toggle" href="https://geneontology.org/docs/introduction-to-go" id="nav02" data-toggle="dropdown" aria-haspopup="true" aria-expanded="false">About</a>
<div class="dropdown-menu" aria-labelledby="nav02">


<a class="dropdown-item" href="http://geneontology.org/docs/introduction-to-go" title="">About the GO</a>
<a class="dropdown-item" href="http://geneontology.org/docs/whoweare/">Who we are</a>
<a class="dropdown-item" href="http://geneontology.org/docs/collaborations/">Collaborations</a>
<a class="dropdown-item" href="http://geneontology.org/docs/annotation-contributors">Annotation contributors</a>
<a class="dropdown-item" href="http://geneontology.org/docs/literature/">Scientific literature</a>
<a class="dropdown-item" href="http://geneontology.org/docs/go-citation-policy/">GO citation policy and license</a>
<a class="dropdown-item" href="https://geneontology.org/docs/introduction-to-go" title="">About the GO</a>
<a class="dropdown-item" href="https://geneontology.org/docs/whoweare/">Who we are</a>
<a class="dropdown-item" href="https://geneontology.org/docs/collaborations/">Collaborations</a>
<a class="dropdown-item" href="https://geneontology.org/docs/annotation-contributors">Annotation contributors</a>
<a class="dropdown-item" href="https://geneontology.org/docs/literature/">Scientific literature</a>
<a class="dropdown-item" href="https://geneontology.org/docs/go-citation-policy/">GO citation policy and license</a>
</div>
</li>

<li class="nav-item dropdown">
<a class="nav-link dropdown-toggle" href="http://geneontology.org/page/downloads" id="nav03" data-toggle="dropdown" aria-haspopup="true" aria-expanded="false">Ontology</a>
<a class="nav-link dropdown-toggle" href="https://geneontology.org/page/downloads" id="nav03" data-toggle="dropdown" aria-haspopup="true" aria-expanded="false">Ontology</a>
<div class="dropdown-menu" aria-labelledby="nav03">
<a class="dropdown-item" href="http://geneontology.org/docs/ontology-documentation/" id="nav-crit" aria-haspopup="true" aria-expanded="false">Gene Ontology Overview</a>
<a class="dropdown-item" href="http://geneontology.org/docs/download-mappings/" id="nav-crit" aria-haspopup="true" aria-expanded="false">Cross-references of external classification systems to GO</a>
<a class="dropdown-item" href="http://geneontology.org/docs/go-subset-guide/" id="nav-crit" aria-haspopup="true" aria-expanded="false">Guide to GO subsets</a>
<a class="dropdown-item" href="http://geneontology.org/docs/contributing-to-go-terms/" id="nav-crit" aria-haspopup="true" aria-expanded="false">Contributing to the ontology</a>
<a class="dropdown-item" href="https://geneontology.org/docs/ontology-documentation/" id="nav-crit" aria-haspopup="true" aria-expanded="false">Gene Ontology Overview</a>
<a class="dropdown-item" href="https://geneontology.org/docs/download-mappings/" id="nav-crit" aria-haspopup="true" aria-expanded="false">Cross-references of external classification systems to GO</a>
<a class="dropdown-item" href="https://geneontology.org/docs/go-subset-guide/" id="nav-crit" aria-haspopup="true" aria-expanded="false">Guide to GO subsets</a>
<a class="dropdown-item" href="https://geneontology.org/docs/contributing-to-go-terms/" id="nav-crit" aria-haspopup="true" aria-expanded="false">Contributing to the ontology</a>
</div>
</li>

<li class="nav-item dropdown">
<a class="nav-link dropdown-toggle" href="http://geneontology.org/page/go-community" id="nav04" data-toggle="dropdown" aria-haspopup="true" aria-expanded="false">Annotations</a>
<a class="nav-link dropdown-toggle" href="https://geneontology.org/page/go-community" id="nav04" data-toggle="dropdown" aria-haspopup="true" aria-expanded="false">Annotations</a>
<div class="dropdown-menu" aria-labelledby="nav04">
<a class="dropdown-item" href="http://geneontology.org/docs/go-annotations/" id="nav-crit" aria-haspopup="true" aria-expanded="false">Introduction to GO annotations</a>
<a class="dropdown-item" href="http://geneontology.org/docs/guide-go-evidence-codes/" id="nav-crit" aria-haspopup="true" aria-expanded="false">Guide to GO evidence codes</a>
<a class="dropdown-item" href="http://geneontology.org/docs/contributing-to-go/" id="nav-crit" aria-haspopup="true" aria-expanded="false">Contributing GO annotations</a>
<a class="dropdown-item" href="https://geneontology.org/docs/go-annotations/" id="nav-crit" aria-haspopup="true" aria-expanded="false">Introduction to GO annotations</a>
<a class="dropdown-item" href="https://geneontology.org/docs/guide-go-evidence-codes/" id="nav-crit" aria-haspopup="true" aria-expanded="false">Guide to GO evidence codes</a>
<a class="dropdown-item" href="https://geneontology.org/docs/contributing-to-go/" id="nav-crit" aria-haspopup="true" aria-expanded="false">Contributing GO annotations</a>
</div>
</li>

<li class="nav-item dropdown">
<a class="nav-link dropdown-toggle" href="http://geneontology.org/page/go-tools-registry" id="nav05" data-toggle="dropdown" aria-haspopup="true" aria-expanded="false">Downloads</a>
<a class="nav-link dropdown-toggle" href="https://geneontology.org/page/go-tools-registry" id="nav05" data-toggle="dropdown" aria-haspopup="true" aria-expanded="false">Downloads</a>
<div class="dropdown-menu" aria-labelledby="nav05">

<a class="dropdown-item" href="http://geneontology.org/docs/downloads/" id="nav-crit" aria-haspopup="true" aria-expanded="false">Downloads overview</a>
<a class="dropdown-item" href="http://geneontology.org/docs/download-ontology/" id="nav-crit" aria-haspopup="true" aria-expanded="false">Download ontology</a>
<a class="dropdown-item" href="http://geneontology.org/docs/download-go-annotations/" id="nav-crit" aria-haspopup="true" aria-expanded="false">Download annotations</a>
<a class="dropdown-item" href="http://geneontology.org/docs/download-go-cams/" id="nav-crit" aria-haspopup="true" aria-expanded="false">Download GO-CAMs</a>
<a class="dropdown-item" href="http://geneontology.org/docs/go-archives/" id="nav-crit" aria-haspopup="true" aria-expanded="false">GO Archive</a>
<a class="dropdown-item" href="http://geneontology.org/docs/deprecated-products-and-formats/" id="nav-crit" aria-haspopup="true" aria-expanded="false">Deprecated formats</a>
<a class="dropdown-item" href="https://geneontology.org/docs/downloads/" id="nav-crit" aria-haspopup="true" aria-expanded="false">Downloads overview</a>
<a class="dropdown-item" href="https://geneontology.org/docs/download-ontology/" id="nav-crit" aria-haspopup="true" aria-expanded="false">Download ontology</a>
<a class="dropdown-item" href="https://geneontology.org/docs/download-go-annotations/" id="nav-crit" aria-haspopup="true" aria-expanded="false">Download annotations</a>
<a class="dropdown-item" href="https://geneontology.org/docs/download-go-cams/" id="nav-crit" aria-haspopup="true" aria-expanded="false">Download GO-CAMs</a>
<a class="dropdown-item" href="https://geneontology.org/docs/go-archives/" id="nav-crit" aria-haspopup="true" aria-expanded="false">GO Archive</a>
<a class="dropdown-item" href="https://geneontology.org/docs/deprecated-products-and-formats/" id="nav-crit" aria-haspopup="true" aria-expanded="false">Deprecated formats</a>
</div>
</li>

<li class="nav-item dropdown">
<a class="nav-link dropdown-toggle" href="http://geneontology.org/page/about" id="nav06" data-toggle="dropdown" aria-haspopup="true" aria-expanded="false">Help</a>
<a class="nav-link dropdown-toggle" href="https://geneontology.org/page/about" id="nav06" data-toggle="dropdown" aria-haspopup="true" aria-expanded="false">Help</a>
<div class="dropdown-menu" aria-labelledby="nav06">
<a class="dropdown-item" href="http://geneontology.org/search.html" id="nav-crit" aria-haspopup="true" aria-expanded="false">Search Documentation</a>
<a class="dropdown-item" href="http://geneontology.org/docs/faq/" id="nav-crit" aria-haspopup="true" aria-expanded="false">Frequently Asked Questions</a>
<a class="dropdown-item" href="http://geneontology.org/docs/go-citation-policy/" id="nav-crit" aria-haspopup="true" aria-expanded="false">Citation and Terms</a>
<a class="dropdown-item" href="https://geneontology.org/search.html" id="nav-crit" aria-haspopup="true" aria-expanded="false">Search Documentation</a>
<a class="dropdown-item" href="https://geneontology.org/docs/faq/" id="nav-crit" aria-haspopup="true" aria-expanded="false">Frequently Asked Questions</a>
<a class="dropdown-item" href="https://geneontology.org/docs/go-citation-policy/" id="nav-crit" aria-haspopup="true" aria-expanded="false">Citation and Terms</a>
<a class="dropdown-item" href="http://help.geneontology.org/" id="nav-crit" aria-haspopup="true" aria-expanded="false">Contact us</a>
</div>
</li>
Expand All @@ -118,7 +118,7 @@
<div class="col-xl-12">
<ol class="breadcrumb">
<li class="breadcrumb-item">
<a href="http://geneontology.org/page/downloads">Downloads</a>
<a href="https://geneontology.org/page/downloads">Downloads</a>
</li>
<li class="breadcrumb-item active">Download Annotations</li>
</ol>
Expand Down Expand Up @@ -228,12 +228,12 @@ <h4>Filtered Annotation File Downloads for {{ date }} release</h4>
1999-2023 <a href="http://www.geneontology.org/"
title="The Gene Ontology project website">the Gene
Ontology</a>
(<a href="http://geneontology.org/page/use-and-license">CC-BY
(<a href="https://geneontology.org/page/use-and-license">CC-BY
4.0</a>)<br /><a href="http://help.geneontology.org/"
title="Contact the GO helpdesk">Helpdesk</a>
• <a href="http://geneontology.org/page/go-citation-policy"
• <a href="https://geneontology.org/page/go-citation-policy"
title="How to cite the GO project">Citation/attribution</a>
• <a href="http://geneontology.org/page/use-and-license"
• <a href="https://geneontology.org/page/use-and-license"
title="Terms of use for the GO project">Terms of use</a><br /> Member of
the <a href="http://www.obofoundry.org/" rel="external"
title="Open Biological and Biomedical Ontologies">Open
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