Adding html output type to biothings

biothings/web/api/es/handlers/base_handler.py

@@ -17,24 +17,24 @@ def initialize(self, web_settings):
         Elasticsearch-specific request handlers go here.'''
         super(BaseESRequestHandler, self).initialize(web_settings)
 
-    def _return_data_and_track(self, data, ga_event_data={}, rawquery=False, status_code=200):
+    def _return_data_and_track(self, data, ga_event_data={}, rawquery=False, status_code=200, _format='json'):
         ''' Small function to return a chunk of data and send a google analytics tracking request.'''
         if rawquery:
-            self.return_raw_query_json(data, status_code=status_code)
+            self.return_raw_query_json(data, status_code=status_code, _format=_format)
         else:
-            self.return_json(data, status_code=status_code)
+            self.return_json(data, status_code=status_code, _format=_format)
         self.ga_track(event=self.ga_event_object(ga_event_data))
         self.self_track(data=self.ga_event_object_ret)
         return
 
-    def return_raw_query_json(self, query, status_code=200):
+    def return_raw_query_json(self, query, status_code=200, _format='json'):
         '''Return valid JSON if `rawquery` option is selected.
         This is necessary as queries can span multiple lines (POST)'''
         _ret = query.get('body', {'GET': query.get('bid')})
         if is_str(_ret) and len(_ret.split('\n')) > 1:
-            self.return_json({'body': _ret}, status_code=status_code)
+            self.return_json({'body': _ret}, status_code=status_code, _format=_format)
         else:
-            self.return_json(_ret, status_code=status_code)
+            self.return_json(_ret, status_code=status_code, _format=_format)
 
     def _should_sanitize(self, param, kwargs):
         return ((param in kwargs) and (param in self.kwarg_settings))

biothings/web/api/es/handlers/biothing_handler.py

@@ -94,7 +94,7 @@ def get(self, bid=None):
 
         # return raw query, if requested
         if options.control_kwargs.rawquery:
-            self._return_data_and_track(_query.get('body', {'GET': bid}), rawquery=True)
+            self._return_data_and_track(_query.get('body', {'GET': bid}), rawquery=True, _format=options.control_kwargs.out_format)
             return
 
         _query = self._pre_query_GET_hook(options, _query)
@@ -107,15 +107,15 @@ def get(self, bid=None):
             res = _backend.annotation_GET_query(_query)
         except Exception:
             self.log_exceptions("Error executing query")
-            self.return_json({'success': False, 'error': self.web_settings.ID_NOT_FOUND_TEMPLATE.format(bid=bid)}, status_code=404)
+            self.return_json({'success': False, 'error': self.web_settings.ID_NOT_FOUND_TEMPLATE.format(bid=bid)}, status_code=404, _format=options.control_kwargs.out_format)
             #raise HTTPError(404)
             return
 
         #logging.debug("Raw query result: {}".format(res))
 
         # return raw result if requested
         if options.control_kwargs.raw:
-            self._return_data_and_track(res)
+            self._return_data_and_track(res, _format=options.control_kwargs.out_format)
             return
 
         res = self._pre_transform_GET_hook(options, res)
@@ -129,19 +129,19 @@ def get(self, bid=None):
             res = _result_transformer.clean_annotation_GET_response(res)
         except Exception:
             self.log_exceptions("Error transforming result")
-            self.return_json({'success': False, 'error': self.web_settings.ID_NOT_FOUND_TEMPLATE.format(bid=bid)}, status_code=404)
+            self.return_json({'success': False, 'error': self.web_settings.ID_NOT_FOUND_TEMPLATE.format(bid=bid)}, status_code=404, _format=options.control_kwargs.out_format)
             #raise HTTPError(404)
             return
 
         # return result
         if not res:
-            self.return_json({'success': False, 'error': self.web_settings.ID_NOT_FOUND_TEMPLATE.format(bid=bid)}, status_code=404)
+            self.return_json({'success': False, 'error': self.web_settings.ID_NOT_FOUND_TEMPLATE.format(bid=bid)}, status_code=404, _format=options.control_kwargs.out_format)
             #raise HTTPError(404)
             return
 
         res = self._pre_finish_GET_hook(options, res)
 
-        self._return_data_and_track(res)
+        self._return_data_and_track(res, _format=options.control_kwargs.out_format)
 
     ###########################################################################
 
@@ -170,7 +170,7 @@ def post(self, ids=None):
 
         if not options.control_kwargs.ids:
             self._return_data_and_track({'success': False, 'error': "Missing required parameters."}, 
-                                        ga_event_data={'qsize': 0}, status_code=400)
+                                        ga_event_data={'qsize': 0}, status_code=400, _format=options.control_kwargs.out_format)
             return
 
         options = self._pre_query_builder_POST_hook(options)
@@ -202,7 +202,7 @@ def post(self, ids=None):
         logging.debug("Request query: {}".format(_query))
 
         if options.control_kwargs.rawquery:
-            self._return_data_and_track(_query, ga_event_data={'qsize': len(options.control_kwargs.ids)}, rawquery=True)
+            self._return_data_and_track(_query, ga_event_data={'qsize': len(options.control_kwargs.ids)}, rawquery=True, _format=options.control_kwargs.out_format)
             return
 
         _query = self._pre_query_POST_hook(options, _query)
@@ -216,17 +216,17 @@ def post(self, ids=None):
         except TypeError as e:
             self.log_exceptions("Error executing annotation POST query")
             self._return_data_and_track({'success': False, 'error': 'Error executing query'},
-                            ga_event_data={'qsize': len(options.control_kwargs.ids)}, status_code=400)
+                            ga_event_data={'qsize': len(options.control_kwargs.ids)}, status_code=400, _format=options.control_kwargs.out_format)
             return
         except BiothingSearchError as e:
-            self._return_data_and_track({'success': False, 'error': '{0}'.format(e)}, ga_event_data={'qsize': len(options.control_kwargs.ids)}, status_code=400)
+            self._return_data_and_track({'success': False, 'error': '{0}'.format(e)}, ga_event_data={'qsize': len(options.control_kwargs.ids)}, status_code=400, _format=options.control_kwargs.out_format)
             return
 
         #logging.debug("Raw query result: {}".format(res))
 
         # return raw result if requested
         if options.control_kwargs.raw:
-            self._return_data_and_track(res, ga_event_data={'qsize': len(options.control_kwargs.ids)})
+            self._return_data_and_track(res, ga_event_data={'qsize': len(options.control_kwargs.ids)}, _format=options.control_kwargs.out_format)
             return
 
         res = self._pre_transform_POST_hook(options, res)
@@ -247,4 +247,4 @@ def post(self, ids=None):
         res = self._pre_finish_POST_hook(options, res)
 
         # return and track
-        self._return_data_and_track(res, ga_event_data={'qsize': len(options.control_kwargs.ids)})
+        self._return_data_and_track(res, ga_event_data={'qsize': len(options.control_kwargs.ids)}, _format=options.control_kwargs.out_format)

biothings/web/api/es/handlers/metadata_handler.py

@@ -52,7 +52,7 @@ def get(self):
 
         # return raw query, if requested
         if options.control_kwargs.rawquery:
-            self.return_json({}, rawquery=True)
+            self.return_json({}, rawquery=True, _format=options.control_kwargs.out_format)
             return
 
         _query = self._pre_query_GET_hook(options, _query)
@@ -68,7 +68,7 @@ def get(self):
 
         # return raw result if requested
         if options.control_kwargs.raw:
-            self.return_json(res)
+            self.return_json(res, _format=options.control_kwargs.out_format)
             return
 
         res = self._pre_transform_GET_hook(options, res)
@@ -83,4 +83,4 @@ def get(self):
 
         res = self._pre_finish_GET_hook(options, res)
 
-        self.return_json(res)
+        self.return_json(res, _format=options.control_kwargs.out_format)

biothings/web/api/es/handlers/query_handler.py

@@ -65,7 +65,7 @@ def get(self):
 
         if not options.control_kwargs.q and not options.control_kwargs.scroll_id:
             self._return_data_and_track({'success': False, 'error': "Missing required parameters."},
-                            ga_event_data={'total': 0}, status_code=400)
+                            ga_event_data={'total': 0}, status_code=400, _format=options.control_kwargs.out_format)
             return
 
         options = self._pre_query_builder_GET_hook(options)
@@ -109,7 +109,7 @@ def get(self):
             try:
                 res = _backend.scroll(_query)
             except BiothingScrollError as e:
-                self._return_data_and_track({'success': False, 'error': '{}'.format(e)}, ga_event_data={'total': 0}, status_code=400)
+                self._return_data_and_track({'success': False, 'error': '{}'.format(e)}, ga_event_data={'total': 0}, status_code=400, _format=options.control_kwargs.out_format)
                 return
             #except Exception as e:
             #    self.log_exceptions("Error getting scroll batch")
@@ -119,7 +119,7 @@ def get(self):
             #logging.debug("Raw scroll query result: {}".format(res))
 
             if options.control_kwargs.raw:
-                self._return_data_and_track(res, ga_event_data={'total': res.get('total', 0)})
+                self._return_data_and_track(res, ga_event_data={'total': res.get('total', 0)}, _format=options.control_kwargs.out_format)
                 return
 
             res = self._pre_scroll_transform_GET_hook(options, res)
@@ -131,7 +131,7 @@ def get(self):
             try:
                 res = _result_transformer.clean_scroll_response(res)
             except ScrollIterationDone as e:
-                self._return_data_and_track({'success': False, 'error': '{}'.format(e)}, ga_event_data={'total': res.get('total', 0)}, status_code=200)
+                self._return_data_and_track({'success': False, 'error': '{}'.format(e)}, ga_event_data={'total': res.get('total', 0)}, status_code=200, _format=options.control_kwargs.out_format)
                 return
             #except Exception as e:
             #    self.log_exceptions("Error transforming scroll batch")
@@ -152,7 +152,7 @@ def get(self):
             #    return
 
             if options.control_kwargs.rawquery:
-                self._return_data_and_track(_query, ga_event_data={'total': 0}, rawquery=True)
+                self._return_data_and_track(_query, ga_event_data={'total': 0}, rawquery=True, _format=options.control_kwargs.out_format)
                 return
 
             _query = self._pre_query_GET_hook(options, _query)
@@ -164,7 +164,7 @@ def get(self):
             try:
                 res = _backend.query_GET_query(_query)
             except BiothingSearchError as e:
-                self._return_data_and_track({'success': False, 'error': '{0}'.format(e)}, ga_event_data={'total': 0}, status_code=400)
+                self._return_data_and_track({'success': False, 'error': '{0}'.format(e)}, ga_event_data={'total': 0}, status_code=400, _format=options.control_kwargs.out_format)
                 return
             #except Exception as e:
             #    self.log_exceptions("Error executing query")
@@ -177,7 +177,7 @@ def get(self):
 
             # return raw result if requested
             if options.control_kwargs.raw:
-                self._return_data_and_track(res, ga_event_data={'total': res.get('total', 0)})
+                self._return_data_and_track(res, ga_event_data={'total': res.get('total', 0)}, _format=options.control_kwargs.out_format)
                 return
 
             res = self._pre_transform_GET_hook(options, res)
@@ -199,7 +199,7 @@ def get(self):
         res = self._pre_finish_GET_hook(options, res)
 
         # return and track
-        self.return_json(res)
+        self.return_json(res, _format=options.control_kwargs.out_format)
         if options.control_kwargs.fetch_all:
             self.ga_event_object_ret['action'] = 'fetch_all'
         self.ga_track(event=self.ga_event_object({'total': res.get('total', 0)}))
@@ -231,7 +231,7 @@ def post(self):
 
         if not options.control_kwargs.q:
             self._return_data_and_track({'success': False, 'error': "Missing required parameters."},
-                ga_event_data={'qsize': 0}, status_code=400)
+                ga_event_data={'qsize': 0}, status_code=400, _format=options.control_kwargs.out_format)
             return
 
         options = self._pre_query_builder_POST_hook(options)
@@ -264,7 +264,7 @@ def post(self):
         #    return
 
         if options.control_kwargs.rawquery:
-            self._return_data_and_track(_query, ga_event_data={'qsize': len(options.control_kwargs.q)}, rawquery=True)
+            self._return_data_and_track(_query, ga_event_data={'qsize': len(options.control_kwargs.q)}, rawquery=True, _format=options.control_kwargs.out_format)
             return
 
         _query = self._pre_query_POST_hook(options, _query)
@@ -276,7 +276,7 @@ def post(self):
         try:
             res = _backend.query_POST_query(_query)
         except BiothingSearchError as e:
-            self._return_data_and_track({'success': False, 'error': '{0}'.format(e)}, ga_event_data={'qsize': len(options.control_kwargs.q)}, status_code=400)
+            self._return_data_and_track({'success': False, 'error': '{0}'.format(e)}, ga_event_data={'qsize': len(options.control_kwargs.q)}, status_code=400, _format=options.control_kwargs.out_format)
             return
         #except Exception as e:
         #    self.log_exceptions("Error executing POST query")
@@ -287,7 +287,7 @@ def post(self):
 
         # return raw result if requested
         if options.control_kwargs.raw:
-            self._return_data_and_track(res, ga_event_data={'qsize': len(options.control_kwargs.q)})
+            self._return_data_and_track(res, ga_event_data={'qsize': len(options.control_kwargs.q)}, _format=options.control_kwargs.out_format)
             return
 
         res = self._pre_transform_POST_hook(options, res)
@@ -309,4 +309,4 @@ def post(self):
         res = self._pre_finish_POST_hook(options, res)
 
         # return and track
-        self._return_data_and_track(res, ga_event_data={'qsize': len(options.control_kwargs.q)})
+        self._return_data_and_track(res, ga_event_data={'qsize': len(options.control_kwargs.q)}, _format=options.control_kwargs.out_format)

biothings/web/api/helper.py

@@ -154,7 +154,18 @@ def get_query_params(self):
         _args = self._sanitize_params(_args)
         return _args
 
-    def return_json(self, data, encode=True, indent=None, status_code=200):
+    def return_html(self, data, status_code=200):
+        self.set_status(status_code)
+        if not self.web_settings.DISABLE_CACHING:
+            #get etag if data is a dictionary and has "etag" attribute.
+            etag = data.get('etag', None) if isinstance(data, dict) else None
+            self.set_cacheable(etag=etag)
+        self.support_cors()
+        self.set_header("Content-Type", "text/html; charset=utf-8")
+        self.write(self.web_settings.HTML_OUT_TEMPLATE.format(json.dumps(data)))
+        return
+
+    def return_json(self, data, encode=True, indent=None, status_code=200, _format='json'):
         '''Return passed data object as JSON response.
         If **jsonp** parameter is set in the  request, return a valid 
         `JSONP <https://en.wikipedia.org/wiki/JSONP>`_ response.
@@ -163,8 +174,11 @@ def return_json(self, data, encode=True, indent=None, status_code=200):
         :param encode: if encode is False, assumes input data is already a JSON encoded string.
         :param indent: number of indents per level in JSON string
         :param status_code: HTTP status code for response
+        :param _format: output format - currently either "html" or "json"
         '''    
-        # call the recursive function to sort the data by keys and add the json-ld information
+        if _format == 'html':
+            self.return_html(data, status_code)
+            return
         indent = indent or 2   # tmp settings
         self.set_status(status_code)
         if SUPPORT_MSGPACK and self.web_settings.ENABLE_MSGPACK and getattr(self, 'use_msgpack', False):

biothings/web/settings/default.py

@@ -1,6 +1,7 @@
 from biothings.web.api.es.query import ESQuery as DefaultESQuery
 from biothings.web.api.es.query_builder import ESQueryBuilder as DefaultESQueryBuilder
 from biothings.web.api.es.transform import ESResultTransformer as DefaultESResultTransformer
+from biothings.web.templates import HTML_OUT_TEMPLATE
 import re
 
 # *****************************************************************************
@@ -94,7 +95,8 @@
 
 # For annotation GET endpoint
 ANNOTATION_GET_CONTROL_KWARGS = {'raw': {'default': False, 'type': bool}, 
-                                 'rawquery': {'default': False, 'type': bool}}
+                                 'rawquery': {'default': False, 'type': bool},
+                                 'out_format': {'default': 'json', 'type': str}}
 ANNOTATION_GET_ES_KWARGS = {'_source': {'default': None, 'type': list, 'max': 100, 'alias': ['fields', 'filter']}}
 ANNOTATION_GET_ESQB_KWARGS = {}
 ANNOTATION_GET_TRANSFORM_KWARGS = {'dotfield': {'default': False, 'type': bool}, 
@@ -104,7 +106,8 @@
 # For annotation POST endpoint
 ANNOTATION_POST_CONTROL_KWARGS = {'raw': {'default': False, 'type': bool},
                                   'rawquery': {'default': False, 'type': bool},
-                                  'ids': {'default': None, 'type': list, 'max': 1000}}
+                                  'ids': {'default': None, 'type': list, 'max': 1000},
+                                  'out_format': {'default': 'json', 'type': str}}
 ANNOTATION_POST_ES_KWARGS = {'_source': {'default': None, 'type': list, 'max': 100, 'alias': ['fields', 'filter']}}
 ANNOTATION_POST_ESQB_KWARGS = {}
 ANNOTATION_POST_TRANSFORM_KWARGS = {'dotfield': {'default': False, 'type': bool},
@@ -120,7 +123,8 @@
                                 ]
                             },
                             'scroll_id': {'default': None, 'type': str},
-                            'fetch_all': {'default': False, 'type': bool}}
+                            'fetch_all': {'default': False, 'type': bool},
+                            'out_format': {'default': 'json', 'type': str}}
 QUERY_GET_ES_KWARGS = {'_source': {'default': None, 'type': list, 'max': 100, 'alias': ['fields', 'filter']},
                        'from': {'default': None, 'type': int, 'alias': 'skip'},
                        'size': {'default': None, 'type': int, 'alias': 'limit'},
@@ -137,7 +141,8 @@
 # For query POST endpoint
 QUERY_POST_CONTROL_KWARGS = {'q': {'default': None, 'type': list},
                              'raw': {'default': False, 'type': bool},
-                             'rawquery': {'default': False, 'type': bool}}
+                             'rawquery': {'default': False, 'type': bool},
+                             'out_format': {'default': 'json', 'type': str}}
 QUERY_POST_ES_KWARGS = {'_source': {'default': None, 'type': list, 'max': 100, 'alias': ['fields', 'filter']},
                         'size': {'default': None, 'type': int}}
 QUERY_POST_ESQB_KWARGS = {'scopes': {'default': None, 'type': list, 'max': 100, 
@@ -149,7 +154,7 @@
                                '_sorted': {'default': True, 'type': bool}}
 
 # For metadata GET endpoint
-METADATA_GET_CONTROL_KWARGS = {}
+METADATA_GET_CONTROL_KWARGS = {'out_format': {'default': 'json', 'type': str}}
 METADATA_GET_ES_KWARGS = {}
 METADATA_GET_ESQB_KWARGS = {}
 METADATA_GET_TRANSFORM_KWARGS = {'dev': {'default': False, 'type': bool},