Merge pull request #1877 from josenavas/adding-prep-info

Adding prep template get handler

qiita_db/handlers/prep_template.py

@@ -7,6 +7,7 @@
 # -----------------------------------------------------------------------------
 
 from json import loads
+from os.path import basename
 
 from tornado.web import HTTPError
 import pandas as pd
@@ -46,6 +47,47 @@ def _get_prep_template(pid):
     return pt
 
 
+class PrepTemplateDBHandler(OauthBaseHandler):
+    @authenticate_oauth
+    def get(self, prep_id):
+        """Retrieves the prep template information
+
+        Parameters
+        ----------
+        prep_id: str
+            The id of the prep template whose information is being retrieved
+
+        Returns
+        -------
+        dict
+            The prep information:
+            'data_type': prep info data type
+            'artifact': artifact attached to the given prep
+            'investigation_type': prep info investigation type
+            'study': study that the prep info belongs to
+            'status': prep info status
+            'qiime-map': the path to the qiime mapping file
+            'prep-file': the path to the prep info file
+        """
+        with qdb.sql_connection.TRN:
+            pt = _get_prep_template(prep_id)
+            prep_files = [fp for _, fp in pt.get_filepaths()
+                          if 'qiime' not in basename(fp)]
+            response = {
+                'data_type': pt.data_type(),
+                'artifact': pt.artifact.id,
+                'investigation_type': pt.investigation_type,
+                'study': pt.study_id,
+                'status': pt.status,
+                'qiime-map': pt.qiime_map_fp,
+                # The first element in the prep_files is the newest
+                # prep information file - hence the correct one
+                'prep-file': prep_files[0]
+            }
+
+        self.write(response)
+
+
 class PrepTemplateDataHandler(OauthBaseHandler):
     @authenticate_oauth
     def get(self, prep_id):

qiita_db/handlers/tests/test_prep_template.py

@@ -8,6 +8,8 @@
 
 from unittest import main, TestCase
 from json import loads, dumps
+from os.path import join
+from functools import partial
 
 from tornado.web import HTTPError
 
@@ -27,6 +29,33 @@ def test_get_prep_template(self):
             _get_prep_template(100)
 
 
+class PrepTemplateHandlerTests(OauthTestingBase):
+    def test_get_does_not_exist(self):
+        obs = self.get('/qiita_db/prep_template/100/', headers=self.header)
+        self.assertEqual(obs.code, 404)
+
+    def test_get_no_header(self):
+        obs = self.get('/qiita_db/prep_template/1/')
+        self.assertEqual(obs.code, 400)
+
+    def test_get(self):
+        obs = self.get('/qiita_db/prep_template/1/', headers=self.header)
+        self.assertEqual(obs.code, 200)
+
+        db_test_template_dir = qdb.util.get_mountpoint('templates')[0][1]
+        path_builder = partial(join, db_test_template_dir)
+
+        obs = loads(obs.body)
+        exp = {'data_type': '18S',
+               'artifact': 1,
+               'investigation_type': 'Metagenomics',
+               'study': 1,
+               'status': 'private',
+               'qiime-map': path_builder('1_prep_1_qiime_19700101-000000.txt'),
+               'prep-file': path_builder('1_prep_1_19700101-000000.txt')}
+        self.assertEqual(obs, exp)
+
+
 class PrepTemplateDataHandlerTests(OauthTestingBase):
     def test_get_does_not_exist(self):
         obs = self.get('/qiita_db/prep_template/100/data/',

qiita_pet/webserver.py

@@ -46,7 +46,8 @@
     ProcessingJobAPItestHandler)
 from qiita_db.handlers.artifact import ArtifactHandler
 from qiita_db.handlers.prep_template import (
-    PrepTemplateDataHandler, PrepTemplateAPItestHandler)
+    PrepTemplateDataHandler, PrepTemplateAPItestHandler,
+    PrepTemplateDBHandler)
 from qiita_db.handlers.oauth2 import TokenAuthHandler
 from qiita_db.handlers.reference import ReferenceFilepathsHandler
 from qiita_db.handlers.core import ResetAPItestHandler
@@ -151,6 +152,7 @@ def __init__(self):
             (r"/qiita_db/jobs/(.*)", JobHandler),
             (r"/qiita_db/artifacts/(.*)/", ArtifactHandler),
             (r"/qiita_db/prep_template/(.*)/data/", PrepTemplateDataHandler),
+            (r"/qiita_db/prep_template/(.*)/", PrepTemplateDBHandler),
             (r"/qiita_db/references/(.*)/filepaths/",
              ReferenceFilepathsHandler)
         ]