From 4a7754dd9eb88b9e3192d870cb7d56dc06281395 Mon Sep 17 00:00:00 2001
From: Renzo Frigato <rfrigato@stanford.edu>
Date: Tue, 8 Mar 2016 15:29:17 -0800
Subject: [PATCH] add advanced datatree search query
---
api/api.py | 3 +-
api/handlers/searchhandler.py | 105 +++++++++++++++++++++++++++++++++-
2 files changed, 106 insertions(+), 2 deletions(-)
diff --git a/api/api.py b/api/api.py
index 9f029a00..091febb9 100644
--- a/api/api.py
+++ b/api/api.py
@@ -137,7 +137,8 @@ routes = [
webapp2.Route(_format(r'/api/<par_cont_name:groups>/<par_id:{group_id_re}>/<cont_name:projects>'), containerhandler.ContainerHandler, name='cont_sublist_groups', handler_method='get_all', methods=['GET']),
webapp2.Route(_format(r'/api/<par_cont_name:{cont_name_re}>/<par_id:{cid_re}>/<cont_name:{cont_name_re}>'), containerhandler.ContainerHandler, name='cont_sublist', handler_method='get_all', methods=['GET']),
webapp2.Route(_format(r'/api/search'), searchhandler.SearchHandler, name='es_proxy', methods=['GET']),
- webapp2.Route(_format(r'/api/search/<cont_name:{cont_name_re}>'), searchhandler.SearchHandler, name='es_proxy_1', methods=['GET']),
+ webapp2.Route(_format(r'/api/search/files'), searchhandler.SearchHandler, handler_method='get_datatree', name='es_data', methods=['GET']),
+ webapp2.Route(_format(r'/api/search/<cont_name:{cont_name_re}>'), searchhandler.SearchHandler, name='es_proxy', methods=['GET']),
webapp2.Route(_format(r'/api/schemas/<schema:{schema_re}>'), schemahandler.SchemaHandler, name='schemas', methods=['GET']),
]
diff --git a/api/handlers/searchhandler.py b/api/handlers/searchhandler.py
index 6d109c4a..c92b72be 100644
--- a/api/handlers/searchhandler.py
+++ b/api/handlers/searchhandler.py
@@ -1,3 +1,4 @@
+import bson
import datetime
import elasticsearch
@@ -6,8 +7,77 @@ from .. import config
log = config.log
+parent_container = {
+ 'acquisitions': 'sessions',
+ 'sessions': 'projects'
+}
+
+def _filter_body_by_type(body, doc_type):
+ query = {
+ 'query': {
+ 'filtered': {
+ 'query': body,
+ 'filter': {
+ 'type': {
+ 'value': doc_type
+ }
+ }
+ }
+ },
+ 'min_score': 0.5
+ }
+ return query
class SearchHandler(base.RequestHandler):
+ """This class allows to proxy queries to elasticsearch
+ The get method just wraps the body in a convenient elasticsearch query.
+ The get_datatree (for the special doc_type 'files') for each result build the datatree
+ with the containers in their hierarchy.
+ output example:
+ [
+ {
+ "mimetype": "application/zip",
+ "hash": "v0-sha384-8607a3c17008ff24d0cb9e1ccd60f5c7bcc1810b8c1dc9ee0f14ee91b7b1f897b78fcb035ff0135520a58bebfcdbd78b",
+ "name": "8613_6_1_t1.zip",
+ "project": {
+ "group": "scitran",
+ "created": "2016-03-08T22:46:01.941000+00:00",
+ "modified": "2016-03-08T22:46:33.030000+00:00",
+ "label": "Neuroscience",
+ "_id": "56df5629b13d67a9cbfca1ea",
+ "public": false
+ },
+ "session": {
+ "group": "scitran",
+ "created": "2016-03-08T22:46:16.221000+00:00",
+ "modified": "2016-03-08T22:46:18.822000+00:00",
+ "label": "1.2.840.113619.6.353.50113891957665820485497041858168751557",
+ "project": "56df5629b13d67a9cbfca1ea",
+ "_id": "56df5638b13d67a9cbfca1f7",
+ "public": false,
+ "subject": {
+ "code": "ex8613"
+ }
+ },
+ "container_name": "acquisitions",
+ "type": "dicom",
+ "acquisition": {
+ "created": "2016-03-08T22:46:17.164000",
+ "timestamp": "2015-01-07T17:38:09",
+ "modified": "2016-03-08T22:46:17.164000",
+ "label": "T1_high-res_inplane_Ret_knk",
+ "instrument": "MRI",
+ "session": "56df5638b13d67a9cbfca1f7",
+ "measurement": "anatomical",
+ "timezone": "America/Los_Angeles",
+ "_id": "56df5639b13d67a9cbfca1f9",
+ "public": false
+ },
+ "size": 3216386
+ },
+ ...
+ ]
+ """
def __init__(self, request=None, response=None):
super(SearchHandler, self).__init__(request, response)
@@ -17,8 +87,41 @@ class SearchHandler(base.RequestHandler):
self.abort(403, 'search is available only for authenticated users')
size = self.get_param('size')
body = self.request.json_body
+ query = _filter_body_by_type(body, cont_name)
try:
- results = config.es.search(index='scitran', doc_type=cont_name, body=body, _source=['_id'], size=size or 10)
+ results = config.es.search(index='scitran', body=body, _source=['_id'], size=size or 10)
except elasticsearch.exceptions.ConnectionError as e:
self.abort(503, 'elasticsearch is not available')
return results['hits']['hits']
+
+ def get_datatree(self, **kwargs):
+ if self.public_request:
+ self.abort(403, 'search is available only for authenticated users')
+ size = self.get_param('size')
+ body = self.request.json_body
+ query = _filter_body_by_type(body, 'files')
+ try:
+ es_results = config.es.search(index='scitran', body=query, size=size or 10)
+ ## elastic search results are wrapped in subkey ['hits']['hits']
+ es_results = es_results['hits']['hits']
+ results = []
+ for result in es_results:
+ # extract the source of the result
+ result = result['_source']
+ # add to the result the container hierarchy references
+ container = result.pop('container')
+ container.pop('permissions')
+ cont_name = result['container_name']
+ result[cont_name[:-1]] = container
+ while parent_container.get(cont_name):
+ parent_cont_name = parent_container[cont_name]
+ parent_id = bson.objectid.ObjectId(container[parent_cont_name[:-1]])
+ container = config.db[parent_cont_name].find_one({'_id': parent_id})
+ container.pop('permissions')
+ result[parent_cont_name[:-1]] = container
+ cont_name = parent_cont_name
+ results.append(result)
+ except elasticsearch.exceptions.ConnectionError as e:
+ self.abort(503, 'elasticsearch is not available')
+ return results
+
--
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