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 ++++++++++++++++++++++++++++++++++--
 bh20simplewebuploader/main.py        | 26 -------------------------
 bh20simplewebuploader/static/main.js |  4 ++--
 3 files changed, 37 insertions(+), 30 deletions(-)

(limited to 'bh20simplewebuploader')

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])
diff --git a/bh20simplewebuploader/main.py b/bh20simplewebuploader/main.py
index c306749..62ec5cd 100644
--- a/bh20simplewebuploader/main.py
+++ b/bh20simplewebuploader/main.py
@@ -694,32 +694,6 @@ def getCountDB():
     # print(result, file=sys.stderr)
     return jsonify({'sequences': int(result[0]["num"]["value"])})
 
-# Execute a 'global search'
-@app.route('/api/search', methods=['GET'])
-def search():
-    s = request.args.get('s')
-    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']
-    print(result,file=sys.stderr);
-    return jsonify([{
-        'id': x['id']['value'],
-        'seq': x['seq']['value'],
-        'info': x['info']['value'],
-    } for x in result])
-
 @app.route('/api/getAllaccessions', methods=['GET'])
 def getAllaccessions():
     query="""SELECT DISTINCT ?fasta ?value WHERE {?fasta ?x[ <http://edamontology.org/data_2091> ?value ]}"""
diff --git a/bh20simplewebuploader/static/main.js b/bh20simplewebuploader/static/main.js
index a12311e..c0bc23f 100644
--- a/bh20simplewebuploader/static/main.js
+++ b/bh20simplewebuploader/static/main.js
@@ -19,11 +19,11 @@ function toDIVTable(rows) {
         html = '<div class="rTable">';
         rows.forEach(row => {
             id = row['id'];
-            seq = row['seq'];
             info = row['info'];
             html += '<div class="rTableRow">';
             html += cell('<a href="'+info+'">'+id+'</a>');
-            html += cell('<a href="'+seq+'">FASTA</a>');
+            html += cell('<a href="'+row['collection']+'">Collection</a>');
+            html += cell('<a href="'+row['fasta']+'">FASTA</a>');
             html += cell('<a href="/api/ebi/sample-'+id+'.xml">EBI/ENA export XML</a>');
             html += '</div>';
         });
-- 
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