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author | lltommy | 2020-11-11 09:56:12 +0100 |
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committer | lltommy | 2020-11-11 09:56:12 +0100 |
commit | d6aa323b6fc7a82e45cc1df51fc72c2d547146eb (patch) | |
tree | 6e8b77bde4dc34fab3fa8804906f3cb821f61dae /bh20simplewebuploader/main.py | |
parent | c5fe5de7e4c77bfb48b1ae2f662c2d9cc120c06e (diff) | |
parent | c872248e43c1c66e5fed8ef341f7b4ac21d63e6f (diff) | |
download | bh20-seq-resource-d6aa323b6fc7a82e45cc1df51fc72c2d547146eb.tar.gz bh20-seq-resource-d6aa323b6fc7a82e45cc1df51fc72c2d547146eb.tar.lz bh20-seq-resource-d6aa323b6fc7a82e45cc1df51fc72c2d547146eb.zip |
Merge branch 'master' of https://github.com/arvados/bh20-seq-resource
Diffstat (limited to 'bh20simplewebuploader/main.py')
-rw-r--r-- | bh20simplewebuploader/main.py | 53 |
1 files changed, 48 insertions, 5 deletions
diff --git a/bh20simplewebuploader/main.py b/bh20simplewebuploader/main.py index 73503b4..1d7154c 100644 --- a/bh20simplewebuploader/main.py +++ b/bh20simplewebuploader/main.py @@ -7,6 +7,7 @@ import logging import os import sys import re +import redis import string import ruamel.yaml as yaml import pkg_resources @@ -252,8 +253,19 @@ def send_home(): """ Send the front page. """ - - return render_template('home.html', menu='HOME', load_map=True) + redis_client = redis.Redis(host=os.environ.get('HOST', 'localhost'), + port=os.environ.get('PORT', 6379), + db=os.environ.get('REDIS_DB', 0)) + tweets = [] + for tweet_id in redis_client.zrevrange('bh20-tweet-score:', + 0, -1): + tweets.append( + {k.decode("utf-8"): v.decode("utf-8") for k, v in + redis_client.hgetall(tweet_id).items()} + ) + return render_template('home.html', menu='HOME', + tweets=tweets, + load_map=True) @app.route('/upload') @@ -675,13 +687,32 @@ 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 . +}} +union +{{ + ?sequenceuri <http://biohackathon.org/bh20-seq-schema/collection_pdh> "{id}" . + ?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 . @@ -699,8 +730,9 @@ 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'] @@ -715,7 +747,18 @@ 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 |