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-rw-r--r--bh20simplewebuploader/api.py116
-rw-r--r--bh20simplewebuploader/main.py26
-rw-r--r--bh20simplewebuploader/static/main.css1
-rw-r--r--bh20simplewebuploader/templates/home.html71
4 files changed, 161 insertions, 53 deletions
diff --git a/bh20simplewebuploader/api.py b/bh20simplewebuploader/api.py
index b1b505f..761ad03 100644
--- a/bh20simplewebuploader/api.py
+++ b/bh20simplewebuploader/api.py
@@ -3,20 +3,26 @@
import os
import requests
import sys
+import types
from flask import Flask, request, redirect, send_file, send_from_directory, render_template, jsonify
from bh20simplewebuploader.main import app, sparqlURL
+PUBSEQ="http://covid19.genenetwork.org"
+ARVADOS="https://collections.lugli.arvadosapi.com/c="
+
# Helper functions
-def fetch_sample_metadata(id):
- query = """
+def fetch_sample(id, query=None):
+ default_query = """
+
PREFIX pubseq: <http://biohackathon.org/bh20-seq-schema#MainSchema/>
PREFIX sio: <http://semanticscience.org/resource/>
PREFIX edam: <http://edamontology.org/>
PREFIX efo: <http://www.ebi.ac.uk/efo/>
PREFIX evs: <http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#>
PREFIX obo: <http://purl.obolibrary.org/obo/>
+
select distinct ?id ?seq ?date ?info ?specimen ?sequencer ?mapper
{
?sample sio:SIO_000115 "%s" ;
@@ -24,15 +30,49 @@ def fetch_sample_metadata(id):
evs:C25164 ?date .
?seq pubseq:technology ?tech ;
pubseq:sample ?sample .
- ?tech efo:EFO_0002699 ?mapper ;
- obo:OBI_0600047 ?sequencer .
+ optional { ?tech efo:EFO_0002699 ?mapper } .
+ optional { ?tech obo:OBI_0600047 ?sequencer . }
optional { ?sample edam:data_2091 ?info } .
optional { ?sample obo:OBI_0001479 ?specimen } .
} limit 5
+
""" % id
+ if not query: query = default_query
+ print(query)
payload = {'query': query, 'format': 'json'}
r = requests.get(sparqlURL, params=payload)
- return r.json()['results']['bindings']
+ res = r.json()
+ print(res)
+ return res['results']['bindings'],res['head']['vars']
+
+def fetch_one_sample(id, query=None):
+ """Get the top sample and return a SimpleNamespace"""
+
+ result,varlist = fetch_sample(id,query)
+ h = {}
+ row = result[0]
+ for key in varlist:
+ if key in row:
+ h[key] = row[key]['value']
+ print(h)
+ h['arv_id'] = os.path.basename(h['seq'])
+ return types.SimpleNamespace(**h)
+
+def fetch_one_record(id):
+ m = fetch_one_sample(id)
+ arv_id = m.arv_id
+ rec = { "id": id,
+ 'arv_id': arv_id,
+ "permalink": PUBSEQ+'/resource/'+id,
+ "collection": m.seq,
+ 'collection_date': m.date,
+ 'fasta': ARVADOS+arv_id+'/sequence.fasta',
+ 'metadata': ARVADOS+arv_id+'/metadata.yaml',
+ }
+ h = m.__dict__ # for optional items
+ if 'mapper' in h: rec['mapper'] = m.mapper
+ if 'sequencer' in h: rec['sequencer']= m.sequencer
+ return rec
# Main API routes
@@ -42,54 +82,40 @@ def version():
@app.route('/api/sample/<id>.json')
def sample(id):
- # metadata = file.name(seq)+"/metadata.yaml"
- meta = fetch_sample_metadata(id)
- print(meta)
- return jsonify([{
- 'id': x['id']['value'],
- 'fasta': x['seq']['value'],
- 'collection': os.path.dirname(x['seq']['value']),
- 'date': x['date']['value'],
- 'info': x['info']['value'],
- 'specimen': x['specimen']['value'],
- 'sequencer': x['sequencer']['value'],
- 'mapper': x['mapper']['value'],
- } for x in meta])
+ """
+
+API sample should return a record pointing to other resources,
+notably: permalink, original metadata record and the fasta
+data.
+
+curl http://localhost:5067/api/sample/MT533203.1.json
+{
+ "id": "MT533203.1",
+ "permalink": "http://covid19.genenetwork.org/resource/MT533203.1",
+ "collection": "http://covid19.genenetwork.org/resource/lugli-4zz18-uovend31hdwa5ks",
+ "collection_date": "2020-04-27",
+ "fasta": "https://collections.lugli.arvadosapi.com/c=lugli-4zz18-uovend31hdwa5ks/sequence.fasta",
+ "metadata": "https://collections.lugli.arvadosapi.com/c=lugli-4zz18-uovend31hdwa5ks/metadata.yaml",
+ "mapper": "minimap v. 2.17",
+ "sequencer": "http://www.ebi.ac.uk/efo/EFO_0008632"
+}
+
+"""
+
+ return jsonify([fetch_one_record(id)])
@app.route('/api/ebi/sample-<id>.xml', methods=['GET'])
def ebi_sample(id):
- meta = fetch_sample_metadata(id)[0]
+ meta,varlist = fetch_sample(id)[0]
page = render_template('ebi-sample.xml',sampleid=id,sequencer=meta['sequencer']['value'],date=meta['date']['value'],specimen=meta['specimen']['value'])
return page
@app.route('/api/search', methods=['GET'])
def search():
"""
- Execute a 'global search'
+ Execute a 'global search'. Currently just duplicates fetch one
+ sample. Should be more flexible FIXME.
"""
s = request.args.get('s')
- if s == "":
- s = "MT326090.1"
- query = """
- PREFIX pubseq: <http://biohackathon.org/bh20-seq-schema#MainSchema/>
- PREFIX sio: <http://semanticscience.org/resource/>
- PREFIX edam: <http://edamontology.org/>
- select distinct ?id ?seq ?info
- {
- ?sample sio:SIO_000115 "%s" .
- ?sample sio:SIO_000115 ?id .
- ?seq pubseq:sample ?sample .
- ?sample edam:data_2091 ?info .
- } limit 100
- """ % s
- payload = {'query': query, 'format': 'json'}
- r = requests.get(sparqlURL, params=payload)
- result = r.json()['results']['bindings']
- # metadata = file.name(seq)+"/metadata.yaml"
- print(result)
- return jsonify([{
- 'id': x['id']['value'],
- 'fasta': x['seq']['value'],
- 'collection': os.path.dirname(x['seq']['value']),
- 'info': x['info']['value'],
- } for x in result])
+ if s == "": s = "MT326090.1"
+ return jsonify([fetch_one_record(s)])
diff --git a/bh20simplewebuploader/main.py b/bh20simplewebuploader/main.py
index b620946..504f03c 100644
--- a/bh20simplewebuploader/main.py
+++ b/bh20simplewebuploader/main.py
@@ -34,6 +34,7 @@ if not os.path.isfile('bh20sequploader/main.py'):
print("WARNING: run FLASK from the root of the source repository!", file=sys.stderr)
app = Flask(__name__, static_url_path='/static', static_folder='static')
+app.config['JSON_SORT_KEYS'] = False
# Limit file upload size. We shouldn't be working with anything over 1 MB; these are small genomes.
# We will enforce the limit ourselves and set a higher safety limit here.
@@ -252,7 +253,7 @@ FORM_ITEMS = load_schema_generate_form()
def get_feed_items(name, start=0, stop=9):
redis_client = redis.Redis(host=os.environ.get('HOST', 'localhost'),
port=os.environ.get('PORT', 6379),
- db=os.environ.get('REDIS_DB', 0))
+ db=os.environ.get('REDIS_DB', 0))
feed_items = []
try:
for el in redis_client.zrevrange(name, start, stop):
@@ -272,12 +273,23 @@ def send_home():
"""
Send the front page.
"""
+ (tweets,
+ commits,
+ pubmed_articles,
+ arxiv_articles) = [get_feed_items(x) for x in ["bh20-tweet-score:",
+ "bh20-commit-score:",
+ "bh20-pubmed-score:",
+ "bh20-arxiv-score:"]]
return render_template(
'home.html', menu='HOME',
- tweets=get_feed_items("bh20-tweet-score:"),
- commits=get_feed_items("bh20-commit-score:"),
- pubmed_articles=get_feed_items("bh20-pubmed-score:"),
- arxiv_articles=get_feed_items("bh20-arxiv-score:"),
+ all_items=list(itertools.chain(tweets,
+ commits,
+ pubmed_articles,
+ arxiv_articles)),
+ tweets=tweets,
+ commits=commits,
+ pubmed_articles=pubmed_articles,
+ arxiv_articles=arxiv_articles,
load_map=True)
@@ -750,8 +762,8 @@ union
# http://covid19.genenetwork.org/resource/lugli-4zz18-gx0ifousk9yu0ql
m = re.match(r"http://collections.lugli.arvadosapi.com/c=([^/]*)/sequence.fasta|http://covid19.genenetwork.org/resource/(.*)", sequenceuri)
collection = m.group(1) or m.group(2)
- fastauri = f"http://collections.lugli.arvadosapi.com/c={collection}/sequence.fasta"
- metauri = f"http://collections.lugli.arvadosapi.com/c={collection}/metadata.yaml"
+ fastauri = f"https://collections.lugli.arvadosapi.com/c={collection}/sequence.fasta"
+ metauri = f"https://collections.lugli.arvadosapi.com/c={collection}/metadata.yaml"
locationuri=sample['geo']['value']
location=sample['geoname']['value']
date=sample['date']['value']
diff --git a/bh20simplewebuploader/static/main.css b/bh20simplewebuploader/static/main.css
index fbc721e..e2f0c83 100644
--- a/bh20simplewebuploader/static/main.css
+++ b/bh20simplewebuploader/static/main.css
@@ -567,6 +567,7 @@ input[name="feed-tabs"] ~ .tab {
display: none;
}
+#tab-all-items:checked ~ .tab.content-all-items,
#tab-pubmed-articles:checked ~ .tab.content-pubmed-articles,
#tab-arxiv-articles:checked ~ .tab.content-arxiv-articles,
#tab-tweets:checked ~ .tab.content-tweets,
diff --git a/bh20simplewebuploader/templates/home.html b/bh20simplewebuploader/templates/home.html
index a880f81..23f48bf 100644
--- a/bh20simplewebuploader/templates/home.html
+++ b/bh20simplewebuploader/templates/home.html
@@ -29,7 +29,9 @@
</div>
<div id="feed">
- <input name="feed-tabs" type="radio" id="tab-arxiv-articles" checked/>
+ <input name="feed-tabs" type="radio" id="tab-all-items" checked/>
+ <label for="tab-all-items">All Items</label>
+ <input name="feed-tabs" type="radio" id="tab-arxiv-articles"/>
<label for="tab-arxiv-articles">Arxiv</label>
<input name="feed-tabs" type="radio" id="tab-pubmed-articles"/>
<label for="tab-pubmed-articles">Pubmed</label>
@@ -37,6 +39,73 @@
<label for="tab-tweets">Tweets</label>
<input name="feed-tabs" type="radio" id="tab-commits"/>
<label for="tab-commits">Commits</label>
+ <ul class="tab content-all-items">
+ <!-- Begin News -->
+ {% if all_items %}
+ {% for item in all_items|sort(reverse=true, attribute="score")%}
+ <li>
+ {% if item['authors'] %}
+ <!-- Arxiv article -->
+ <p>
+ <b>[arxiv]</b>
+ <a href="{{ item['url'] }}" target="_blank">
+ {{item['title']}}
+ </a>
+ <br/>
+ <b>Authors:</b> {{ item['authors'] }}
+ <br/>
+ <b>Abstract:</b> {{ item['abstract']}}...
+ <br/>
+ <b>Submitted:</b> {{ item['submission']}}
+ </p>
+
+ {% elif item['full-authors'] %}
+ <!-- Pubmed Article -->
+ <p><b>[Pubmed]:</b>
+ <a href="https://pubmed.ncbi.nlm.nih.gov/{{ item['docsum-pmid'] }}" target="_blank"><b>Summary:</b>
+ {{ item['summary'] }}
+ </a> <br/>
+ <b>Full Authors:</b> {{ item['full-authors'] }} <br/>
+ <b>Short Authors:</b> {{ item['short-authors'] }} <br/>
+ <b>Citation:</b> {{ item['citation'] }} <br/>
+ <b>Short Journal Citation:</b> {{ item['short-journal-citation'] }} <br/>
+ </p>
+
+ {% elif item['tweet'] %}
+ <!-- Tweets -->
+ <p>
+ <b>[Tweet]:</b>
+ {{ item['tweet']|urlize(40, target="_blank")}}
+ <small>
+ <a href="{{ item['url'] }}" target="_blank">source</a></small>
+ <br/>
+ by {{ item['author'] }}
+ <br/>
+ <small>{{ item['timeposted'] }}</small>
+ </p>
+
+ {% elif item['repository-url'] %}
+ <!-- Commits -->
+ <p>
+ <b>[Commit]:</b>
+ <a href="{{ item.url }}" target="_blank">
+ {{ item.hash.split(":")[-1][:7] }}: {{ item.content }}
+ </a>
+ <br/>
+ <small>
+ <a href="{{ item['repository-url'] }}" target="_blank"> {{ item.author }}/{{ item.repository }}</a>
+ on {{ item.timeposted }}
+ </small>
+ </p>
+ {% endif %}
+ </li>
+ {%endfor%}
+
+ {% else %}
+ There are no items to display :(
+ {% endif %}
+ <!-- End News -->
+ </ul>
<ul class="tab content-arxiv-articles">
{% if arxiv_articles %}
{% for article in arxiv_articles|sort(reverse=true, attribute="score")%}