diff options
Diffstat (limited to 'bh20simplewebuploader')
| -rw-r--r-- | bh20simplewebuploader/main.py | 25 |
1 files changed, 17 insertions, 8 deletions
diff --git a/bh20simplewebuploader/main.py b/bh20simplewebuploader/main.py index e88eb4c..53a4cda 100644 --- a/bh20simplewebuploader/main.py +++ b/bh20simplewebuploader/main.py @@ -8,7 +8,7 @@ import re import string import yaml import pkg_resources -from flask import Flask, request, redirect, send_file, send_from_directory, render_template +from flask import Flask, request, redirect, send_file, send_from_directory, render_template, jsonify import os.path import requests @@ -358,7 +358,8 @@ def getAllaccessions(): payload = {'query': query, 'format': 'json'} r = requests.get(baseURL, params=payload) result = r.json()['results']['bindings'] - return str(result) + return jsonify([{'uri': x['fasta']['value'], + 'value': x['value']['value']} for x in result]) # parameter must be encoded e.g. http://arvados.org/keep:6e6276698ed8b0e6cd21f523e4f91179+123/sequence.fasta must become @@ -368,11 +369,12 @@ def getDetailsForSeq(): seq_id = request.args.get('seq') query="""SELECT DISTINCT ?key ?value WHERE {<placeholder> ?x [?key ?value]}""" query=query.replace("placeholder", seq_id) - print(query) payload = {'query': query, 'format': 'json'} r = requests.get(baseURL, params=payload) result = r.json()['results']['bindings'] - return str(result) + return jsonify([{'uri': x['key']['value'], + 'value': x['value']['value']} for x in result]) + @app.route('/api/getSEQbytech', methods=['GET']) def getSEQbytech(): @@ -384,7 +386,9 @@ def getSEQbytech(): payload = {'query': query, 'format': 'json'} r = requests.get(baseURL, params=payload) result = r.json()['results']['bindings'] - return str(result) + return jsonify([{'Fasta Count': x['fastaCount']['value'], + 'Specimen Source': x['specimen_source']['value'], + 'Label': x['specimen_source_label']['value']} for x in result]) @app.route('/api/getSEQbyLocation', methods=['GET']) def getSEQbyLocation(): @@ -396,7 +400,10 @@ def getSEQbyLocation(): payload = {'query': query, 'format': 'json'} r = requests.get(baseURL, params=payload) result = r.json()['results']['bindings'] - return str(result) + return jsonify([{'Fasta Count': x['fastaCount']['value'], + 'GeoLocation': x['geoLocation']['value'], + 'GeoLocation Label': x['geoLocation_label']['value']} for x in result]) + @app.route('/api/getSEQbySpecimenSource', methods=['GET']) def getSEQbySpecimenSource(): @@ -409,7 +416,9 @@ def getSEQbySpecimenSource(): payload = {'query': query, 'format': 'json'} r = requests.get(baseURL, params=payload) result = r.json()['results']['bindings'] - return str(result) + return jsonify([{'Fasta Count': x['fastaCount']['value'], + 'Specimen Source': x['specimen_source']['value'], + 'Label': x['specimen_source_label']['value']} for x in result]) #No data for this atm @app.route('/api/getSEQbyHostHealthStatus', methods=['GET']) @@ -423,4 +432,4 @@ def getSEQbyHostHealthStatus(): payload = {'query': query, 'format': 'json'} r = requests.get(baseURL, params=payload) result = r.json()['results']['bindings'] - return str(result)
\ No newline at end of file + return str(result) |