Merge branch 'master' of github.com:arvados/bh20-seq-resource

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)
\ No newline at end of file