Use dsl query builder signature

src/web/api/handlers.py

@@ -1,105 +1,96 @@
-# -*- coding: utf-8 -*-
-from biothings.web.api.es.handlers import BiothingHandler
-from biothings.web.api.es.handlers import MetadataHandler
-from biothings.web.api.es.handlers import QueryHandler
-from biothings.web.api.es.handlers import StatusHandler
-from biothings.utils.version import get_repository_information
-from tornado.web import RequestHandler
-from collections import OrderedDict
-import requests
-import os
-
-#import logging
-
-
-def get_es_index(inst, options):
-    return inst.web_settings.ES_INDEX
-    # if 'all' in options.esqb_kwargs.species or len(set(options.esqb_kwargs.species)-
-    #    set([x['tax_id'] for x in inst.web_settings.TAXONOMY.values()])) > 0:
-    #    return inst.web_settings.ES_INDEX
-    # else:
-    #    return inst.web_settings.ES_INDEX_TIER1
-
-
-class FrontPageHandler(BiothingHandler):
-    def get(self):
-        self.write("MYGENE FRONTPAGE!")
-
 
-class GeneHandler(BiothingHandler):
-    ''' This class is for the /gene endpoint. '''
+import requests
 
-    def _get_es_index(self, options):
-        return get_es_index(self, options)
+from biothings.utils.version import (get_repository_information,
+                                     get_software_info)
+from biothings.web.api.es.handlers import (QueryHandler,
+                                           MetadataFieldHandler,
+                                           MetadataSourceHandler)
 
 
-class QueryHandler(QueryHandler):
+class MygeneQueryHandler(QueryHandler):
     ''' This class is for the /query endpoint. '''
 
-    def _pre_query_builder_GET_hook(self, options):
-        if options.esqb_kwargs.include_tax_tree and 'all' not in options.esqb_kwargs.species:
-            headers = {
-                'user-agent': 'Python-requests_mygene.info/{} (gzip)'.format(requests.__version__)}
-
-            body = {
-                "ids": ','.join([str(sid) for sid in options.esqb_kwargs.species]),
-                "expand_species": 'True'
-            }
+    def pre_query_builder_hook(self, options):
 
-            res = requests.post(
-                self.web_settings.INCLUDE_TAX_TREE_REDIRECT_ENDPOINT, data=body, headers=headers)
+        if self.request.method == 'GET':
+            if options.esqb.include_tax_tree and \
+                    'all' not in options.esqb.species:
+                headers = {
+                    'user-agent': 'Python-requests_mygene.info/{} (gzip)'.format(requests.__version__)}
 
-            if res.status_code == requests.codes.ok:
-                options['esqb_kwargs']['species'] = [str(x) for x in res.json()]
-                # logging.debug('tax_tree species: {}'.format(options.esqb_kwargs.species))
-
-        return options
+                body = {
+                    "ids": ','.join([str(sid) for sid in options.esqb.species]),
+                    "expand_species": 'True'
+                }
 
-    def _get_es_index(self, options):
-        return get_es_index(self, options)
+                res = requests.post(
+                    self.web_settings.INCLUDE_TAX_TREE_REDIRECT_ENDPOINT, data=body, headers=headers)
 
+                if res.status_code == requests.codes.ok:
+                    options['esqb']['species'] = [str(x) for x in res.json()]
+                    # logging.debug('tax_tree species: {}'.format(options.esqb_kwargs.species))
 
-class StatusHandler(StatusHandler):
-    ''' This class is for the /status endpoint. '''
-    pass
+        return options
 
 
-class MetadataHandler(MetadataHandler):
-    ''' This class is for the /metadata endpoint. '''
+class MygeneSourceHandler(MetadataSourceHandler):
+    """
+    GET /metadata
+    GET /v3/metadata
+
+    {
+        "app_revision": "", # TODO
+        "available_fields": "http://mygene.info/metadata/fields",
+        "biothing_type": "gene",
+        "build_date": "2020-03-29T04:00:00.012426",
+        "build_version": "20200329",
+        "genome_assembly": {
+            "human": "hg38",
+            "mouse": "mm10",
+            ...
+        },
+        "source": null,
+        "src": { ... }, // 28 items
+        "stats": {
+            "total": 36232158,
+            "total_genes": 36232158,
+            "total_entrez_genes": 27119488,
+            "total_ensembl_genes": 38915576,
+            "total_ensembl_genes_mapped_to_entrez": 5954466,
+            "total_ensembl_only_genes": 9112670,
+            "total_species": 28605
+        },
+        "taxonomy": {
+            "human": 9606,
+            "mouse": 10090,
+            ...
+        }
+    }
+    """
 
-    def _pre_finish_GET_hook(self, options, res):
-        if not self.request.path.endswith('fields'):
-            # Add mygene specific metadata stuff
-            res['available_fields'] = 'http://mygene.info/metadata/fields'
-            res['app_revision'] = get_repository_information(
-                app_dir=self.web_settings._app_git_repo).get(
-                'commit-hash', '')
-            res['genome_assembly'] = {}
-            res['taxonomy'] = {}
-            for (s, d) in self.web_settings.TAXONOMY.items():
-                if 'tax_id' in d:
-                    res['taxonomy'][s] = int(d['tax_id'])
-                if 'assembly' in d:
-                    res['genome_assembly'][s] = d['assembly']
-            if "source" not in res:
-                # occurs when loaded from scratch, not from a change/diff file
-                res["source"] = None
-            res = OrderedDict(sorted(list(res.items()), key=lambda x: x[0]))
-        return res
+    def get(self):
 
+        self.web_settings.read_index_mappings()
+        res = self.web_settings.source_metadata[self.biothing_type]
+        software = get_software_info(app_dir=self.web_settings.get_git_repo_path())
 
-class TaxonHandler(RequestHandler):
-    def initialize(self, web_settings):
-        pass
+        if self.kwargs.source.dev:
+            res['software'] = software
 
-    def get(self, taxid):
-        self.redirect("http://t.biothings.io/v1/taxon/%s?include_children=1" % taxid)
+        res['available_fields'] = 'http://mygene.info/metadata/fields'
+        res['app_revision'] = software.get('commit-hash', '')
+        res['genome_assembly'] = {}
+        res['taxonomy'] = {}
 
+        for s, d in self.web_settings.TAXONOMY.items():
+            if 'tax_id' in d:
+                res['taxonomy'][s] = int(d['tax_id'])
+            if 'assembly' in d:
+                res['genome_assembly'][s] = d['assembly']
 
-class DemoHandler(RequestHandler):
-    def initialize(self, web_settings):
-        pass
+        if "source" not in res:
+            # occurs when loaded from scratch, not from a change/diff file
+            res["source"] = None
 
-    def get(self):
-        with open('../docs/demo/index.html', 'r') as demo_file:
-            self.write(demo_file.read())
+        self.finish(dict(sorted(res.items())))