Merge branch 'death-march' of github.com:eldeveloper/qiita into death-march

Author: wasade

qiita_db/study.py

@@ -1240,7 +1240,6 @@ def from_name_and_affiliation(cls, name, affiliation):
             qdb.sql_connection.TRN.add(sql, [name, affiliation])
             return cls(int(qdb.sql_connection.TRN.execute_fetchlast()))
 
-
     @classmethod
     def create(cls, name, email, affiliation, address=None, phone=None):
         """Create a StudyPerson object, checking if person already exists.

qiita_db/test/test_study.py

@@ -46,12 +46,11 @@ def test_delete(self):
         self.assertFalse(
             qdb.study.StudyPerson.exists('SomeDude', 'affil'))
 
-    def test_retrieve_non_existant_person(self):
-        with self.assertRaises(qdb.esceptions.QiitaDBLookupError):
+    def test_retrieve_non_existant_people(self):
+        with self.assertRaises(qdb.exceptions.QiitaDBLookupError):
             qdb.study.StudyPerson.from_name_and_affiliation('Boaty McBoatFace',
                                                             'UCSD')
 
-    def test_retrieve_non_existant_person(self):
         p = qdb.study.StudyPerson.from_name_and_affiliation('LabDude',
                                                             'knight lab')
         self.assertEqual(p.name, 'LabDude')

qiita_pet/handlers/rest/rest_handler.py

@@ -12,14 +12,17 @@
 
 
 class RESTHandler(BaseHandler):
+    def fail(self, msg, status):
+        self.write({'message': msg})
+        self.set_status(status)
+        self.finish()
+
     def study_boilerplate(self, study_id):
         study_id = to_int(study_id)
         s = None
         try:
             s = Study(study_id)
         except QiitaDBUnknownIDError:
-            self.set_status(404)
-            self.write({'message': 'Study not found'})
-            self.finish()
+            self.fail('Study not found', 404)
         finally:
             return s

qiita_pet/handlers/rest/study.py

@@ -17,7 +17,6 @@
 
 
 class StudyHandler(RESTHandler):
-    # /api/v1/study/<int>
 
     @authenticate_oauth
     def get(self, study_id):
@@ -45,23 +44,20 @@ def get(self, study_id):
 
 
 class StudyCreatorHandler(RESTHandler):
+
     @authenticate_oauth
     def post(self, *args, **kwargs):
         try:
             payload = json_decode(self.request.body)
         except ValueError:
-            self.set_status(400)
-            self.write({'message': 'Could not parse body'})
-            self.finish()
+            self.fail('Could not parse body', 400)
             return
 
         required = {'title', 'study_abstract', 'study_description',
                     'study_alias', 'owner', 'efo', 'contacts'}
 
         if not required.issubset(payload):
-            self.set_status(400)
-            self.write({'message': 'Not all required arguments provided'})
-            self.finish()
+            self.fail('Not all required arguments provided', 400)
             return
 
         title = payload['title']
@@ -71,9 +67,7 @@ def post(self, *args, **kwargs):
 
         owner = payload['owner']
         if not User.exists(owner):
-            self.set_status(403)
-            self.write({'message': 'Unknown user'})
-            self.finish()
+            self.fail('Unknown user', 403)
             return
         else:
             owner = User(owner)
@@ -82,27 +76,21 @@ def post(self, *args, **kwargs):
         contacts = payload['contacts']
 
         if Study.exists(title):
-            self.set_status(409)
-            self.write({'message': 'Study title already exists'})
-            self.finish()
+            self.fail('Study title already exists', 409)
             return
 
         pi_name = contacts['principal_investigator'][0]
         pi_aff = contacts['principal_investigator'][1]
         if not StudyPerson.exists(pi_name, pi_aff):
-            self.set_status(403)
-            self.write({'message': 'Unknown principal investigator'})
-            self.finish()
+            self.fail('Unknown principal investigator', 403)
             return
         else:
             pi = StudyPerson.from_name_and_affiliation(pi_name, pi_aff)
 
         lp_name = contacts['lab_person'][0]
         lp_aff = contacts['lab_person'][1]
         if not StudyPerson.exists(lp_name, lp_aff):
-            self.set_status(403)
-            self.write({'message': 'Unknown lab person'})
-            self.finish()
+            self.fail('Unknown lab person', 403)
             return
         else:
             lp = StudyPerson.from_name_and_affiliation(lp_name, lp_aff)

qiita_pet/handlers/rest/study_person.py

@@ -21,9 +21,7 @@ def get(self, *args, **kwargs):
         try:
             p = StudyPerson.from_name_and_affiliation(name, affiliation)
         except QiitaDBLookupError:
-            self.set_status(404)
-            self.write({'message': 'Person not found'})
-            self.finish()
+            self.fail('Person not found', 404)
             return
 
         self.write({'address': p.address, 'phone': p.phone, 'email': p.email,
@@ -40,9 +38,7 @@ def post(self, *args, **kwargs):
         address = self.get_argument('address', None)
 
         if StudyPerson.exists(name, affiliation):
-            self.set_status(409)
-            self.write({'message': 'Person already exists'})
-            self.finish()
+            self.fail('Person already exists', 409)
             return
 
         p = StudyPerson.create(name=name, affiliation=affiliation, email=email,

qiita_pet/handlers/rest/study_preparation.py

@@ -9,7 +9,7 @@
 import os
 
 import pandas as pd
-from tornado.escape import json_encode, json_decode
+from tornado.escape import json_decode
 
 from qiita_db.util import get_mountpoint
 from qiita_db.artifact import Artifact
@@ -21,7 +21,6 @@
 
 
 class StudyPrepCreatorHandler(RESTHandler):
-    # /api/v1/study/<int>/preparation/
     # TODO: do something smart about warnings, perhaps this should go in its
     # own endpoint i.e. /api/v1/study/<int>/preparation/validate
 
@@ -41,9 +40,7 @@ def post(self, study_id, *args, **kwargs):
             p = PrepTemplate.create(data, study_id, data_type,
                                     investigation_type)
         except QiitaError as e:
-            self.write(json_encode({'message': e.message}))
-            self.set_status(406)
-            self.finish()
+            self.fail(e.message, 406)
             return
 
         self.write({'id': p.id})
@@ -52,7 +49,7 @@ def post(self, study_id, *args, **kwargs):
 
 
 class StudyPrepArtifactCreatorHandler(RESTHandler):
-    # /api/v1/study/<int>/preparation/<int>/artifact
+
     @authenticate_oauth
     def post(self, study_id, prep_id):
         study = self.study_boilerplate(study_id)
@@ -63,16 +60,11 @@ def post(self, study_id, prep_id):
         try:
             p = PrepTemplate(prep_id)
         except QiitaDBUnknownIDError:
-            self.set_status(404)
-            self.write({'message': 'Preparation not found'})
-            self.finish()
+            self.fail('Preparation not found', 404)
             return
 
         if p.study_id != study.id:
-            self.set_status(409)
-            self.write({'message': 'Preparation ID not associated with the '
-                                   'study'})
-            self.finish()
+            self.fail('Preparation ID not associated with the study', 409)
             return
 
         artifact_deets = json_decode(self.request.body)
@@ -87,9 +79,7 @@ def post(self, study_id, prep_id):
                                   artifact_deets['artifact_name'],
                                   p)
         except QiitaError as e:
-            self.write(json_encode({'message': e.message}))
-            self.set_status(406)
-            self.finish()
+            self.fail(e.message, 406)
             return
 
         self.write({'id': art.id})

qiita_pet/handlers/rest/study_samples.py

@@ -12,7 +12,6 @@
 
 
 class StudySamplesHandler(RESTHandler):
-    # /api/v1/study/<int>/samples
 
     @authenticate_oauth
     def get(self, study_id):
@@ -30,17 +29,12 @@ def get(self, study_id):
 
 
 class StudySamplesCategoriesHandler(RESTHandler):
-    # /api/v1/study/<int>/samples?foo
-
-    def _err(self, msg, status):
-        self.write({'message': msg})
-        self.set_status(status)
-        self.finish()
 
     @authenticate_oauth
     def get(self, study_id, categories):
         if not categories:
-            return self._err('No categories specified', 405)
+            self.fail('No categories specified', 405)
+            return
 
         study = self.study_boilerplate(study_id)
         if study is None:
@@ -49,11 +43,13 @@ def get(self, study_id, categories):
         categories = categories.split(',')
 
         if study.sample_template is None:
-            return self._err('Category not found', 404)
+            self.fail('Category not found', 404)
+            return
 
         available_categories = set(study.sample_template.categories())
         if not set(categories).issubset(available_categories):
-            return self._err('Category not found', 404)
+            self.fail('Category not found', 404)
+            return
 
         blob = {'header': categories,
                 'samples': {}}
@@ -66,7 +62,6 @@ def get(self, study_id, categories):
 
 
 class StudySamplesInfoHandler(RESTHandler):
-    # /api/v1/study/<int>/samples/info
 
     @authenticate_oauth
     def get(self, study_id):

qiita_pet/webserver.py

@@ -57,13 +57,8 @@
     ReloadPluginAPItestHandler)
 from qiita_pet import uimodules
 from qiita_db.util import get_mountpoint
-if qiita_config.portal == "QIITA":
-    from qiita_pet.handlers.portal import (
-        StudyPortalHandler, StudyPortalAJAXHandler)
-
-from qiita_pet.handlers.rest import (
-    StudyHandler as WeDontKnowWhatToCallThis)
 from qiita_pet.handlers.rest import (
+    StudyHandler as WeDontKnowWhatToCallThis,
     StudySamplesHandler as WeDontKnowWhatToCallThisJr,
     StudySamplesInfoHandler as WeDontKnowWhatToCallThisJrJr,
     StudySamplesCategoriesHandler as WeDontKnowWhatToCallThisTheFourth,
@@ -72,6 +67,9 @@
     StudyPrepCreatorHandler as MonsiourWeDontKnowWhatToCallThis,
     StudyPrepArtifactCreatorHandler as FranklyMadamWeDontKnowWhatToCallThis,
     StudyStatusHandler as BondJamesBond)
+if qiita_config.portal == "QIITA":
+    from qiita_pet.handlers.portal import (
+        StudyPortalHandler, StudyPortalAJAXHandler)
 
 
 DIRNAME = dirname(__file__)
@@ -181,7 +179,8 @@ def __init__(self):
             # start of REST API URIs
             (r"/api/v1/study$", WeDontKnowWhatToCallThisSr),
             (r"/api/v1/study/([0-9]+)", WeDontKnowWhatToCallThis),
-            (r"/api/v1/study/([0-9]+)/samples/categories=([a-zA-Z\-0-9\.:,_]*)",
+            (r"/api/v1/study/([0-9]+)/samples/"
+             r"categories=([a-zA-Z\-0-9\.:,_]*)",
                 WeDontKnowWhatToCallThisTheFourth),
             (r"/api/v1/study/([0-9]+)/samples", WeDontKnowWhatToCallThisJr),
             (r"/api/v1/study/([0-9]+)/samples/info",