From 56b5c444fd10cc569c4c0d7b76d034799ce679f9 Mon Sep 17 00:00:00 2001
From: Pjotr Prins
Date: Tue, 21 Jul 2020 09:28:43 +0100
Subject: Working on search

---
 bh20simplewebuploader/api.py | 37 +++++++++++++++++++++++++++++++++++--
 1 file changed, 35 insertions(+), 2 deletions(-)

(limited to 'bh20simplewebuploader/api.py')

diff --git a/bh20simplewebuploader/api.py b/bh20simplewebuploader/api.py
index 8bd1a22..29fa2b8 100644
--- a/bh20simplewebuploader/api.py
+++ b/bh20simplewebuploader/api.py
@@ -1,10 +1,11 @@
 # Public API for PubSeq
 
-import sys
+import os
 import requests
+import sys
 
 from flask import Flask, request, redirect, send_file, send_from_directory, render_template, jsonify
-from bh20simplewebuploader.main import app
+from bh20simplewebuploader.main import app, baseURL
 
 @app.route('/api/version')
 def version():
@@ -14,3 +15,35 @@ def version():
 def ebi_sample(id):
     page = render_template('ebi-sample.xml',**locals())
     return page
+
+@app.route('/api/search', methods=['GET'])
+def search():
+    """
+    Execute a 'global search'
+    """
+    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(baseURL, 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])
-- 
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