Add prep test API creation (#1872)

* Adding prep template data handler to REST api * Adding creation endpoint for prep info * flake8ing * Addressing @antgonza's comments
qiita-spots · Jun 29, 2016 · 3932dc6 · 3932dc6
1 parent 15a03de
commit 3932dc6
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Showing 3 changed files with 48 additions and 3 deletions.
diff --git a/qiita_db/handlers/prep_template.py b/qiita_db/handlers/prep_template.py
@@ -6,7 +6,10 @@
 # The full license is in the file LICENSE, distributed with this software.
 # -----------------------------------------------------------------------------
 
+from json import loads
+
 from tornado.web import HTTPError
+import pandas as pd
 
 import qiita_db as qdb
 from .oauth2 import OauthBaseHandler, authenticate_oauth
@@ -63,3 +66,16 @@ def get(self, prep_id):
             response = {'data': pt.to_dataframe().to_dict(orient='index')}
 
         self.write(response)
+
+
+class PrepTemplateAPItestHandler(OauthBaseHandler):
+    @authenticate_oauth
+    def post(self):
+        prep_info_dict = loads(self.get_argument('prep_info'))
+        study = self.get_argument('study')
+        data_type = self.get_argument('data_type')
+
+        metadata = pd.DataFrame.from_dict(prep_info_dict, orient='index')
+        pt = qdb.metadata_template.prep_template.PrepTemplate.create(
+            metadata, qdb.study.Study(study), data_type)
+        self.write({'prep': pt.id})
diff --git a/qiita_db/handlers/tests/test_prep_template.py b/qiita_db/handlers/tests/test_prep_template.py
@@ -7,7 +7,7 @@
 # -----------------------------------------------------------------------------
 
 from unittest import main, TestCase
-from json import loads
+from json import loads, dumps
 
 from tornado.web import HTTPError
 
@@ -96,5 +96,32 @@ def test_get(self):
             'target_subfragment': 'V4'}
         self.assertEqual(obs, exp)
 
+
+class PrepTemplateAPItestHandlerTests(OauthTestingBase):
+    database = True
+
+    def test_post(self):
+        metadata_dict = {
+            'SKB8.640193': {'primer': 'GTGCCAGCMGCCGCGGTAA',
+                            'barcode': 'GTCCGCAAGTTA',
+                            'platform': 'ILLUMINA',
+                            'instrument_model': 'Illumina MiSeq'},
+            'SKD8.640184': {'primer': 'GTGCCAGCMGCCGCGGTAA',
+                            'barcode': 'GTCCGCAAGTTA',
+                            'platform': 'ILLUMINA',
+                            'instrument_model': 'Illumina MiSeq'}}
+        data = {'prep_info': dumps(metadata_dict),
+                'study': 1,
+                'data_type': '16S'}
+        obs = self.post('/apitest/prep_template/', headers=self.header,
+                        data=data)
+        self.assertEqual(obs.code, 200)
+        obs = loads(obs.body)
+        self.assertEqual(obs.keys(), ['prep'])
+
+        pt = qdb.metadata_template.prep_template.PrepTemplate(obs['prep'])
+        self.assertItemsEqual(pt.keys(), ['1.SKB8.640193', '1.SKD8.640184'])
+
+
 if __name__ == '__main__':
     main()
diff --git a/qiita_pet/webserver.py b/qiita_pet/webserver.py
@@ -45,7 +45,8 @@
     JobHandler, HeartbeatHandler, ActiveStepHandler, CompleteHandler,
     ProcessingJobAPItestHandler)
 from qiita_db.handlers.artifact import ArtifactHandler
-from qiita_db.handlers.prep_template import PrepTemplateDataHandler
+from qiita_db.handlers.prep_template import (
+    PrepTemplateDataHandler, PrepTemplateAPItestHandler)
 from qiita_db.handlers.oauth2 import TokenAuthHandler
 from qiita_db.handlers.reference import ReferenceFilepathsHandler
 from qiita_db.handlers.core import ResetAPItestHandler
@@ -165,7 +166,8 @@ def __init__(self):
             # We add the endpoints for testing plugins
             test_handlers = [
                 (r"/apitest/processing_job/", ProcessingJobAPItestHandler),
-                (r"/apitest/reset/", ResetAPItestHandler)
+                (r"/apitest/reset/", ResetAPItestHandler),
+                (r"/apitest/prep_template/", PrepTemplateAPItestHandler)
             ]
             handlers.extend(test_handlers)