diff options
Diffstat (limited to 'bh20simplewebuploader/main.py')
| -rw-r--r-- | bh20simplewebuploader/main.py | 127 |
1 files changed, 115 insertions, 12 deletions
diff --git a/bh20simplewebuploader/main.py b/bh20simplewebuploader/main.py index e88eb4c..126b8dd 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 @@ -197,6 +197,14 @@ def generate_form(schema, options): record['type'] = 'number' # Choose a reasonable precision for the control record['step'] = '0.0001' + + ### This is to fix the homepage for the moment ## needs more love though + # implementation of the [] stuff instead of just text fields + ## ToDo - implement lists + elif field_type == 'string[]': + record['type'] = 'text' + elif field_type == 'float[]': + record['type'] = 'text' else: raise NotImplementedError('Unimplemented field type {} in {} in metadata schema'.format(field_type, type_name)) yield record @@ -358,7 +366,8 @@ 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 @@ -368,26 +377,69 @@ 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 jsonify([{'uri': x['key']['value'], + 'value': x['value']['value']} for x in result]) + + +@app.route('/api/getSEQCountbytech', methods=['GET']) +def getSEQCountbytech(): + query="""SELECT ?tech ?tech_label (count(?fasta) as ?fastaCount) WHERE + {?fasta ?x [<http://purl.obolibrary.org/obo/OBI_0600047> ?tech] + BIND (concat(?tech,"_label") as ?tech_label)} + GROUP BY ?tech ?tech_label ORDER BY DESC (?fastaCount) + """ + payload = {'query': query, 'format': 'json'} + r = requests.get(baseURL, params=payload) + result = r.json()['results']['bindings'] + return jsonify([{'Fasta Count': x['fastaCount']['value'], + 'tech': x['tech']['value'], + 'Label': x['tech_label']['value']} for x in result]) + +## Is this one really necessary or should we just use getSEQCountbytech instead? +@app.route('/api/getAvailableTech', methods=['GET']) +def getAvailableTech(): + query="""SELECT distinct ?tech ?tech_label WHERE + {?fasta ?x [<http://purl.obolibrary.org/obo/OBI_0600047> ?tech] + BIND (concat(?tech,"_label") as ?tech_label) + } """ payload = {'query': query, 'format': 'json'} r = requests.get(baseURL, params=payload) result = r.json()['results']['bindings'] return str(result) +## List all Sequences/submissions by a given tech, as example e.g. http://purl.obolibrary.org/obo/OBI_0000759 +## Has to be encoded again so should be --> http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FOBI_0000759 @app.route('/api/getSEQbytech', methods=['GET']) def getSEQbytech(): - query="""SELECT ?specimen_source ?specimen_source_label (count(?fasta) as ?fastaCount) WHERE - {?fasta ?x [<http://purl.obolibrary.org/obo/OBI_0600047> ?specimen_source] - BIND (concat(?specimen_source,"_label") as ?specimen_source_label)} - GROUP BY ?specimen_source ?specimen_source_label ORDER BY DESC (?fastaCount) + query="""SELECT ?fasta WHERE + {?fasta ?x [<http://purl.obolibrary.org/obo/OBI_0600047> <placeholder>] } """ + tech = request.args.get('tech') + query=query.replace("placeholder", tech) payload = {'query': query, 'format': 'json'} r = requests.get(baseURL, params=payload) result = r.json()['results']['bindings'] return str(result) + +## Example location, encoded http%3A%2F%2Fwww.wikidata.org%2Fentity%2FQ1223 @app.route('/api/getSEQbyLocation', methods=['GET']) def getSEQbyLocation(): + query="""SELECT ?fasta WHERE {?fasta ?x[ <http://purl.obolibrary.org/obo/GAZ_00000448> <placeholder>]}""" + location=request.args.get('location') + query=query.replace("placeholder", location) + print(query) + payload = {'query': query, 'format': 'json'} + r = requests.get(baseURL, params=payload) + result = r.json()['results']['bindings'] + return str(result) + + +@app.route('/api/getSEQCountbyLocation', methods=['GET']) +def getSEQCountbyLocation(): query="""SELECT ?geoLocation ?geoLocation_label (count(?fasta) as ?fastaCount) WHERE {?fasta ?x [<http://purl.obolibrary.org/obo/GAZ_00000448> ?geoLocation] BIND (concat(?geoLocation,"_label") as ?geoLocation_label)} @@ -396,10 +448,13 @@ 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(): + +@app.route('/api/getSEQCountbySpecimenSource', methods=['GET']) +def getSEQCountbySpecimenSource(): query="""SELECT ?specimen_source ?specimen_source_label (count(?fasta) as ?fastaCount) WHERE {?fasta ?x [<http://purl.obolibrary.org/obo/OBI_0001479> ?specimen_source] BIND (concat(?specimen_source,"_label") as ?specimen_source_label)} @@ -409,11 +464,27 @@ def getSEQbySpecimenSource(): payload = {'query': query, 'format': 'json'} r = requests.get(baseURL, params=payload) result = r.json()['results']['bindings'] + return jsonify([{'Fasta Count': x['fastaCount']['value'], + 'Specimen Source': x['specimen_source']['value'], + 'Label': x['specimen_source_label']['value']} for x in result]) + +# Example specimen http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FNCIT_C155831 +@app.route('/api/getSEQbySpecimenSource', methods=['GET']) +def getSEQBySpecimenSource(): + query="""SELECT ?fasta ?specimen_source ?specimen_source_label WHERE + {?fasta ?x [<http://purl.obolibrary.org/obo/OBI_0001479> <placeholder>] + BIND (concat(?specimen_source,"_label") as ?specimen_source_label)} + """ + specimen=request.args.get('specimen') + query = query.replace("placeholder", specimen) + payload = {'query': query, 'format': 'json'} + r = requests.get(baseURL, params=payload) + result = r.json()['results']['bindings'] return str(result) #No data for this atm -@app.route('/api/getSEQbyHostHealthStatus', methods=['GET']) -def getSEQbyHostHealthStatus(): +@app.route('/api/getSEQCountbyHostHealthStatus', methods=['GET']) +def getSEQCountbyHostHealthStatus(): query="""SELECT ?health_status ?health_status_label (count(?fasta) as ?fastaCount) WHERE {?fasta ?x [<http://purl.obolibrary.org/obo/NCIT_C25688> ?health_status] BIND (concat(?health_status,"_label") as ?health_status_label)} @@ -423,4 +494,36 @@ def getSEQbyHostHealthStatus(): payload = {'query': query, 'format': 'json'} r = requests.get(baseURL, params=payload) result = r.json()['results']['bindings'] + return str(result) + +@app.route('/api/getSEQbyLocationAndTech', methods=['GET']) +def getSEQbyLocationAndTech(): + query="""SELECT ?fasta WHERE { ?fasta ?x [ + <http://purl.obolibrary.org/obo/GAZ_00000448> <placeholderLoc>; <http://purl.obolibrary.org/obo/OBI_0600047> <placeholderTech> ]}""" + location=request.args.get('location') + tech=request.args.get('tech') + query=query.replace("placeholderLoc", location) + query = query.replace("placeholderTech", tech) + print(query) + payload = {'query': query, 'format': 'json'} + r = requests.get(baseURL, params=payload) + result = r.json()['results']['bindings'] + return str(result) + + +# Example Location http%3A%2F%2Fwww.wikidata.org%2Fentity%2FQ1223 +# Example specimen http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FNCIT_C155831 +@app.route('/api/getSEQbyLocationAndSpecimenSource', methods=['GET']) +def getSEQbyLocationAndSpecimenSource(): + query="""SELECT ?fasta WHERE { ?fasta ?x [ + <http://purl.obolibrary.org/obo/GAZ_00000448> <placeholderLoc>; <http://purl.obolibrary.org/obo/OBI_0001479> <placeholderSpecimen> ]} + """ + location = request.args.get('location') + specimen = request.args.get('specimen') + query = query.replace("placeholderLoc", location) + query = query.replace("placeholderSpecimen", specimen) + print(query) + payload = {'query': query, 'format': 'json'} + r = requests.get(baseURL, params=payload) + result = r.json()['results']['bindings'] return str(result)
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