diff options
Diffstat (limited to 'bh20simplewebuploader')
| -rw-r--r-- | bh20simplewebuploader/main.py | 32 | ||||
| -rw-r--r-- | bh20simplewebuploader/static/main.js | 6 | ||||
| -rw-r--r-- | bh20simplewebuploader/templates/blog.html | 5 | ||||
| -rw-r--r-- | bh20simplewebuploader/templates/home.html | 2 | ||||
| -rw-r--r-- | bh20simplewebuploader/templates/menu.html | 2 | ||||
| -rw-r--r-- | bh20simplewebuploader/templates/resource.html | 4 |
6 files changed, 41 insertions, 10 deletions
diff --git a/bh20simplewebuploader/main.py b/bh20simplewebuploader/main.py index 510df1c..fc145e6 100644 --- a/bh20simplewebuploader/main.py +++ b/bh20simplewebuploader/main.py @@ -687,13 +687,27 @@ sparqlURL='http://sparql.genenetwork.org/sparql/' @app.route('/resource/<id>') def resource(id): """Get a COVID19 resource using identifier""" + query=f""" PREFIX pubseq: <http://biohackathon.org/bh20-seq-schema#MainSchema/> PREFIX sio: <http://semanticscience.org/resource/> select distinct ?sample ?geoname ?date ?source ?geo ?sampletype ?institute ?sequenceuri +where {{ {{ ?sample sio:SIO_000115 "{id}" . ?sequenceuri pubseq:sample ?sample . +}} +union +{{ + <http://collections.lugli.arvadosapi.com/c={id}/sequence.fasta> pubseq:sample ?sample . + ?sequenceuri pubseq:sample ?sample . +}} +union +{{ + <http://covid19.genenetwork.org/resource/{id}> pubseq:sample ?sample . + ?sequenceuri pubseq:sample ?sample . +}} + ?sample <http://purl.obolibrary.org/obo/GAZ_00000448> ?geo . ?geo rdfs:label ?geoname . ?sample <http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C25164> ?date . @@ -711,8 +725,9 @@ select distinct ?sample ?geoname ?date ?source ?geo ?sampletype ?institute ?sequ logging.info("^^^^^^^^^^^^^^^^^^^^^^^^^^^^") # return jsonify({'sequences': int(result[0]["num"]["value"])}) sequenceuri=sample['sequenceuri']['value'] - collectionuri=sequenceuri.split('sequence.fasta')[0] - metauri=collectionuri+'metadata.yaml' + m = re.match(r"http://collections.lugli.arvadosapi.com/c=([^/]*)/sequence.fasta|http://covid19.genenetwork.org/resource/(.*)", sequenceuri) + fastauri = "http://collections.lugli.arvadosapi.com/c=%s/sequence.fasta" % m.group(1) + metauri = "http://collections.lugli.arvadosapi.com/c=%s/metadata.yaml" % m.group(1) locationuri=sample['geo']['value'] location=sample['geoname']['value'] date=sample['date']['value'] @@ -727,7 +742,18 @@ select distinct ?sample ?geoname ?date ?source ?geo ?sampletype ?institute ?sequ institute='' if 'institute' in sample: institute=sample['institute']['value'] - return render_template('permalink.html',id=id,menu='',uri=f"http://covid19.genenetwork.org/resource/{id}",sequenceuri=sequenceuri,locationuri=locationuri,location=location,date=date,source=source,sampletype=sampletype,institute=institute,collectionuri=collectionuri,metauri=metauri) + return render_template('permalink.html', + id=id, + menu='', + uri=f"http://covid19.genenetwork.org/resource/{id}", + sequenceuri=fastauri, + locationuri=locationuri, + location=location, + date=date, + source=source, + sampletype=sampletype, + institute=institute, + metauri=metauri) # http://covid19.genenetwork.org/location?label=http://www.wikidata.org/entity/Q114 # http://localhost:5067/location?label=http://www.wikidata.org/entity/Q114 diff --git a/bh20simplewebuploader/static/main.js b/bh20simplewebuploader/static/main.js index 89bc603..6cc0d9f 100644 --- a/bh20simplewebuploader/static/main.js +++ b/bh20simplewebuploader/static/main.js @@ -68,6 +68,12 @@ function fetchHTMLTable(apiEndPoint) { htmlString="<table>" for (var i=0; i<data.length;i++) { let url = data[i]["key"]; + continents = ["Q538", "Q48", "Q49", "Q18", "Q15", "Q27611" ]; + node = url.split("/").pop(); + console.log(continents.includes(node)); + if (url.includes("wikidata") && !continents.includes(node)) { + url = "http://covid19.genenetwork.org/location?label="+url ; + } let label = data[i]["label"]; htmlString=htmlString+"<tr><td><a href=\""+url+"\">"+label+"</a></td><td>"+data[i]["count"]+"<td></tr>" } diff --git a/bh20simplewebuploader/templates/blog.html b/bh20simplewebuploader/templates/blog.html index 88ce4c3..fa08f5b 100644 --- a/bh20simplewebuploader/templates/blog.html +++ b/bh20simplewebuploader/templates/blog.html @@ -9,12 +9,11 @@ {{ embed|safe }} <hr> - <h1>Other blog entries</h1> + <h1>Other documents</h1> {% else %} - {% include 'blurb.html' %} - <h2>BLOG Entries:</h2> + <h2>Documents:</h2> {% endif %} <section class="blog-entries"> diff --git a/bh20simplewebuploader/templates/home.html b/bh20simplewebuploader/templates/home.html index 516fb33..be948f6 100644 --- a/bh20simplewebuploader/templates/home.html +++ b/bh20simplewebuploader/templates/home.html @@ -91,7 +91,7 @@ URI's</a> for <a href="https://en.wikipedia.org/wiki/Wikipedia:Disambiguation">disambiguation</a> and machine readable metadata. For examples of - use, see the <a href="/blog">BLOG</a>. + use, see the <a href="/blog">docs</a>. </p> </div> </section> diff --git a/bh20simplewebuploader/templates/menu.html b/bh20simplewebuploader/templates/menu.html index 5d5fdc8..8e6ef52 100644 --- a/bh20simplewebuploader/templates/menu.html +++ b/bh20simplewebuploader/templates/menu.html @@ -6,7 +6,7 @@ <a href="/status" class="{{ 'active' if menu=='STATUS' }}">STATUS</a> <a href="/demo" class="{{ 'active' if menu=='DEMO' }}">DEMO</a> <a href="/export" class="{{ 'active' if menu=='EXPORT' }}">EXPORT</a> - <a href="/blog" class="{{ 'active' if menu=='BLOG' }}">BLOG</a> + <a href="/blog" class="{{ 'active' if menu=='BLOG' }}">DOCS</a> <a href="/about" class="{{ 'active' if menu=='ABOUT' }}">ABOUT</a> <a href="/contact" class="{{ 'active' if menu=='CONTACT' }}">CONTACT</a> <a href="javascript:void(0);" class="icon" onclick="myFunction()"> diff --git a/bh20simplewebuploader/templates/resource.html b/bh20simplewebuploader/templates/resource.html index fc52f13..4c50fb9 100644 --- a/bh20simplewebuploader/templates/resource.html +++ b/bh20simplewebuploader/templates/resource.html @@ -10,8 +10,8 @@ <p><a href="https://workbench.lugli.arvadosapi.com/projects/lugli-j7d0g-5ct8p1i1wrgyjvp#Data_collections">All sequences project</a></p> <p><a href="https://workbench.lugli.arvadosapi.com/collections/lugli-4zz18-z513nlpqm03hpca/relabeledSeqs.sorted_by_quality_and_len.fasta">All sequences (FASTA) relabled and deduplicated</a></p> <p><a href="https://workbench.lugli.arvadosapi.com/collections/lugli-4zz18-z513nlpqm03hpca/mergedmetadata.ttl">Metadata (RDF) for all sequences</a></p> - <p><a href="https://workbench.lugli.arvadosapi.com/collections/lugli-4zz18-z513nlpqm03hpca/relabeledSeqs.sorted_by_quality_and_len.g6.gfa">All sequences in Graphical Fragment Assembly (GFA)</a> - <a href="https://github.com/GFA-spec/GFA-spec">More about GFA</a></p> - <p><a href="https://workbench.lugli.arvadosapi.com/collections/lugli-4zz18-z513nlpqm03hpca/relabeledSeqs.sorted_by_quality_and_len.g6.unchop.sorted.odgi">All sequences in Optimized Dynamic Genome/Graph Implementation (ODGI)</a> - <a href="https://github.com/vgteam/odgi">More about ODGI</a></p> + <!-- <p><a href="https://workbench.lugli.arvadosapi.com/collections/lugli-4zz18-z513nlpqm03hpca/relabeledSeqs.sorted_by_quality_and_len.g6.gfa">All sequences in Graphical Fragment Assembly (GFA)</a> - <a href="https://github.com/GFA-spec/GFA-spec">More about GFA</a></p> --> + <!-- <p><a href="https://workbench.lugli.arvadosapi.com/collections/lugli-4zz18-z513nlpqm03hpca/relabeledSeqs.sorted_by_quality_and_len.g6.unchop.sorted.odgi">All sequences in Optimized Dynamic Genome/Graph Implementation (ODGI)</a> - <a href="https://github.com/vgteam/odgi">More about ODGI</a></p> --> <!-- <p><a href="https://workbench.lugli.arvadosapi.com/collections/lugli-4zz18-z513nlpqm03hpca/relabeledSeqs_dedup_relabeledSeqs_dedup.ttl.xz">All sequences in RDF using spodgi</a> - <a href="https://github.com/pangenome/spodgi">More about spodgi</a></p> --> |