add: using sparql as interface to workflow

nicholsn · Aug 28, 2014 · 86608fb · 86608fb
1 parent b007078
commit 86608fb
Show file tree

Hide file tree

Showing 6 changed files with 33 additions and 14 deletions.
diff --git a/niquery/app.py b/niquery/app.py
@@ -9,6 +9,7 @@
 from flask import Flask, jsonify, make_response
 from flask.ext.restful import Api, Resource, reqparse
 
+from niquery.utils import NS
 from niquery.query import AskQuery, SelectQuery
 
 
@@ -93,6 +94,8 @@ def bet(in_file_uri):
     return result.provenance.rdf().serialize(format='json-ld')
 
 parser = reqparse.RequestParser()
+parser.add_argument('turtle_file')
+parser.add_argument('query_uuid')
 
 
 class Validate(Resource):
@@ -127,10 +130,20 @@ def get(self, task_id):
 
 class Compute(Resource):
     def get(self):
-        in_file_uri = "http://openfmri.s3.amazonaws.com/ds001/sub001/anatomy/highres001.nii.gz"
-        res = bet.apply_async([in_file_uri])
-        result = {"task_id": res.task_id, "task": "Run FSL BET", "in_file_uri": in_file_uri}
-        return jsonify(result=result)
+        select = SelectQuery()
+        compute = select.sparql_meta.query_type == str(NS.niq.ComputeQuery)
+        result = select.sparql_meta[compute]
+        return result.to_dict(outtype='records')
+
+    def post(self):
+        args = parser.parse_args()
+        select = SelectQuery()
+        input = select.execute(args['query_uuid'], turtle_str=args['turtle_file'])
+        return input.to_dict(outtype='records')
+        #in_file_uri = "http://openfmri.s3.amazonaws.com/ds001/sub001/anatomy/highres001.nii.gz"
+        #res = bet.apply_async([in_file_uri])
+        #result = {"task_id": res.task_id, "task": "Run FSL BET", "in_file_uri": in_file_uri}
+        #return jsonify(result=result)
 
 
 class ComputeResult(Resource):

diff --git a/niquery/query.py b/niquery/query.py
@@ -53,7 +53,10 @@ def _get_sparql_meta(self):
                           format='turtle')
         result = self._graph.query(self._queries['meta.rq'])
         df = utils.result_to_dataframe(result)
-        return df.set_index(df.uri)
+        uuid_series = df.uri.str.slice(start=27)
+        uuid_series.name = 'uuid'
+        uuid = df.join(uuid_series)
+        return uuid.set_index('uuid')
 
     def describe_query(self, index):
         """
@@ -81,7 +84,7 @@ def __init__(self):
         super(SelectQuery, self).__init__()
         self.sparql_meta = self._filter_queries(utils.NS.niq.Select)
 
-    def execute(self, query_index, turtle_file=None, turtle_url=None):
+    def execute(self, query_index, turtle_file=None, turtle_str=None, turtle_url=None):
         """
         Execute a query using the index
 
@@ -98,6 +101,7 @@ def execute(self, query_index, turtle_file=None, turtle_url=None):
         """
         query = self.get_query_string(query_index)
         self._graph.parse(source=turtle_file,
+                          data=turtle_str,
                           location=turtle_url,
                           format='turtle')
         result = self._graph.query(query)
@@ -131,3 +135,4 @@ def execute(self, query_index, turtle_file=None, turtle_url=None):
         result = self._graph.query(query)
         return result.askAnswer
 
+
diff --git a/niquery/sparql/4A5D1346-DDAA-450B-BEA0-B50815FA9766 b/niquery/sparql/4A5D1346-DDAA-450B-BEA0-B50815FA9766
@@ -3,9 +3,10 @@
 PREFIX dcat: <http://www.w3.org/ns/dcat#>
 PREFIX nidm: <http://purl.org/nidash/nidm#>
 
-SELECT DISTINCT ?t1_uri
+SELECT DISTINCT ?t1_uri ?task
 WHERE {
         ?uri a nidm:MriAnatomicalT1 ;
              dcat:downloadURL ?t1_uri ;
              dcat:format nidm:NIFTI1Gzip .
-      }
+      }
+VALUES (?task) {("tasks.bet")}
diff --git a/niquery/sparql/meta.rq b/niquery/sparql/meta.rq
@@ -6,9 +6,9 @@ PREFIX xsd: <http://www.w3.org/2001/XMLSchema#>
 PREFIX nidm: <http://purl.org/nidash/nidm#>
 PREFIX niq: <http://purl.org/niquery#>
 
-SELECT DISTINCT ?uri ?title ?description ?creator ?format ?downloadURL (GROUP_CONCAT(?keyword;SEPARATOR=";") AS ?keywords) ?model
+SELECT DISTINCT ?uri ?title ?description ?query_type ?creator ?format ?downloadURL (GROUP_CONCAT(?keyword;SEPARATOR=";") AS ?keywords) ?model
 WHERE {
-    ?uri a ?query ;
+    ?uri a ?query_type ;
         dct:title ?title ;
         dct:description ?description ;
         dct:creator ?creator ;

diff --git a/niquery/sparql/meta.ttl b/niquery/sparql/meta.ttl
@@ -95,7 +95,7 @@ rq:5F3F3F83-B3D3-4351-90CD-24DA52AE7FE9
     niq:columns      "?subjectID ?tag ?vol ?segID ?annotation ?max ?mean" .
 
 rq:5084B377-F0EC-404F-B18C-942756CC610E
-    a niq:AskQuery ;
+    a niq:ValidationQuery ;
     dct:title        "Validate NIDM Dataset Descriptor Summary-level" ;
     dct:description  "Query a graph to Validate the MUST attributes for the summary level of a descriptor." ;
     dct:creator      <http://orcid.org/0000-0003-1099-3328> ;
@@ -110,8 +110,8 @@ rq:4A5D1346-DDAA-450B-BEA0-B50815FA9766
     dct:title        "Compute BET for every T1 image in the given rdf file" ;
     dct:description  "Query a graph for T1 file URIs in NIfTI GZipped format." ;
     dct:creator      <http://orcid.org/0000-0003-1099-3328> ;
-    dcat:format      niq:SELECT ;
+    dcat:format      niq:Select ;
     dcat:downloadURL <https://raw.githubusercontent.com/nicholsn/niquery/master/niquery/sparql/4A5D1346-DDAA-450B-BEA0-B50815FA9766> ;
     dcat:keyword     "query", "compute", "fsl", "bet" ;
     niq:model        niq:Experiment ;
-    niq:columns      "?t1_uri" .
+    niq:columns      "?t1_uri ?task" .
diff --git a/niquery/utils.py b/niquery/utils.py
@@ -29,7 +29,7 @@ def get_meta_path():
 def get_sparql_queries():
     queries = dict()
     for rq_file in os.listdir(_sparql_path):
-        if rq_file.endswith('.rq'):
+        if not rq_file.endswith('.ttl'):
             rq_path = os.path.join(_sparql_path, rq_file)
             with open(rq_path) as rq:
                 queries.update({rq_file: rq.read()})