Adding prep template data handler to REST api (#1871)

* Adding prep template data handler to REST api

* flake8ing

* Addressing @antgonza's comments

* flake8 - 2, Jose - 0

qiita_db/handlers/prep_template.py

@@ -0,0 +1,65 @@
+# -----------------------------------------------------------------------------
+# Copyright (c) 2014--, The Qiita Development Team.
+#
+# Distributed under the terms of the BSD 3-clause License.
+#
+# The full license is in the file LICENSE, distributed with this software.
+# -----------------------------------------------------------------------------
+
+from tornado.web import HTTPError
+
+import qiita_db as qdb
+from .oauth2 import OauthBaseHandler, authenticate_oauth
+
+
+def _get_prep_template(pid):
+    """Returns the prep template with the given `pid` if it exists
+
+    Parameters
+    ----------
+    pid : str
+        The prep template id
+
+    Returns
+    -------
+    qiita_db.metadata_template.prep_template.PrepTemplate
+        The requested prep template
+
+    Raises
+    ------
+    HTTPError
+        If the prep template does not exist, with error code 404
+        If there is a problem instantiating the template, with error code 500
+    """
+    try:
+        pid = int(pid)
+        pt = qdb.metadata_template.prep_template.PrepTemplate(pid)
+    except qdb.exceptions.QiitaDBUnknownIDError:
+        raise HTTPError(404)
+    except Exception as e:
+        raise HTTPError(500, 'Error instantiating prep template %s: %s'
+                             % (pid, str(e)))
+
+    return pt
+
+
+class PrepTemplateDataHandler(OauthBaseHandler):
+    @authenticate_oauth
+    def get(self, prep_id):
+        """Retrieves the prep contents
+
+        Parameters
+        ----------
+        prep_id : str
+            The id of the prep template whose information is being retrieved
+
+        Returns
+        -------
+        dict
+            The contents of the prep information keyed by sample id
+        """
+        with qdb.sql_connection.TRN:
+            pt = _get_prep_template(prep_id)
+            response = {'data': pt.to_dataframe().to_dict(orient='index')}
+
+        self.write(response)

qiita_db/handlers/tests/test_prep_template.py

@@ -0,0 +1,100 @@
+# -----------------------------------------------------------------------------
+# Copyright (c) 2014--, The Qiita Development Team.
+#
+# Distributed under the terms of the BSD 3-clause License.
+#
+# The full license is in the file LICENSE, distributed with this software.
+# -----------------------------------------------------------------------------
+
+from unittest import main, TestCase
+from json import loads
+
+from tornado.web import HTTPError
+
+from qiita_db.handlers.tests.oauthbase import OauthTestingBase
+import qiita_db as qdb
+from qiita_db.handlers.prep_template import _get_prep_template
+
+
+class UtilTests(TestCase):
+    def test_get_prep_template(self):
+        obs = _get_prep_template(1)
+        exp = qdb.metadata_template.prep_template.PrepTemplate(1)
+        self.assertEqual(obs, exp)
+
+        # It does not exist
+        with self.assertRaises(HTTPError):
+            _get_prep_template(100)
+
+
+class PrepTemplateDataHandlerTests(OauthTestingBase):
+    def test_get_does_not_exist(self):
+        obs = self.get('/qiita_db/prep_template/100/data/',
+                       headers=self.header)
+        self.assertEqual(obs.code, 404)
+
+    def test_get_no_header(self):
+        obs = self.get('/qiita_db/prep_template/100/data/')
+        self.assertEqual(obs.code, 400)
+
+    def test_get(self):
+        obs = self.get('/qiita_db/prep_template/1/data/', headers=self.header)
+        self.assertEqual(obs.code, 200)
+
+        obs = loads(obs.body)
+        self.assertEqual(obs.keys(), ['data'])
+
+        obs = obs['data']
+        exp = ['1.SKB2.640194', '1.SKM4.640180', '1.SKB3.640195',
+               '1.SKB6.640176', '1.SKD6.640190', '1.SKM6.640187',
+               '1.SKD9.640182', '1.SKM8.640201', '1.SKM2.640199',
+               '1.SKD2.640178', '1.SKB7.640196', '1.SKD4.640185',
+               '1.SKB8.640193', '1.SKM3.640197', '1.SKD5.640186',
+               '1.SKB1.640202', '1.SKM1.640183', '1.SKD1.640179',
+               '1.SKD3.640198', '1.SKB5.640181', '1.SKB4.640189',
+               '1.SKB9.640200', '1.SKM9.640192', '1.SKD8.640184',
+               '1.SKM5.640177', '1.SKM7.640188', '1.SKD7.640191']
+        self.assertItemsEqual(obs.keys(), exp)
+
+        obs = obs['1.SKB1.640202']
+        exp = {
+            'barcode': 'GTCCGCAAGTTA',
+            'center_name': 'ANL',
+            'center_project_name': None,
+            'emp_status': 'EMP',
+            'experiment_center': 'ANL',
+            'experiment_design_description':
+                'micro biome of soil and rhizosphere of cannabis plants '
+                'from CA',
+            'experiment_title': 'Cannabis Soil Microbiome',
+            'illumina_technology': 'MiSeq',
+            'instrument_model': 'Illumina MiSeq',
+            'library_construction_protocol':
+                'This analysis was done as in Caporaso et al 2011 Genome '
+                'research. The PCR primers (F515/R806) were developed against '
+                'the V4 region of the 16S rRNA (both bacteria and archaea), '
+                'which we determined would yield optimal community clustering '
+                'with reads of this length using a procedure similar to that '
+                'of ref. 15. [For reference, this primer pair amplifies the '
+                'region 533_786 in the Escherichia coli strain 83972 sequence '
+                '(greengenes accession no. prokMSA_id:470367).] The reverse '
+                'PCR primer is barcoded with a 12-base error-correcting Golay '
+                'code to facilitate multiplexing of up to 1,500 samples per '
+                'lane, and both PCR primers contain sequencer adapter '
+                'regions.',
+            'pcr_primers': 'FWD:GTGCCAGCMGCCGCGGTAA; REV:GGACTACHVGGGTWTCTAAT',
+            'platform': 'Illumina',
+            'primer': 'GTGCCAGCMGCCGCGGTAA',
+            'run_center': 'ANL',
+            'run_date': '8/1/12',
+            'run_prefix': 's_G1_L001_sequences',
+            'samp_size': '.25,g',
+            'sample_center': 'ANL',
+            'sequencing_meth': 'Sequencing by synthesis',
+            'study_center': 'CCME',
+            'target_gene': '16S rRNA',
+            'target_subfragment': 'V4'}
+        self.assertEqual(obs, exp)
+
+if __name__ == '__main__':
+    main()

qiita_pet/webserver.py

@@ -45,6 +45,7 @@
     JobHandler, HeartbeatHandler, ActiveStepHandler, CompleteHandler,
     ProcessingJobAPItestHandler)
 from qiita_db.handlers.artifact import ArtifactHandler
+from qiita_db.handlers.prep_template import PrepTemplateDataHandler
 from qiita_db.handlers.oauth2 import TokenAuthHandler
 from qiita_db.handlers.reference import ReferenceFilepathsHandler
 from qiita_db.handlers.core import ResetAPItestHandler
@@ -148,6 +149,7 @@ def __init__(self):
             (r"/qiita_db/jobs/(.*)/complete/", CompleteHandler),
             (r"/qiita_db/jobs/(.*)", JobHandler),
             (r"/qiita_db/artifacts/(.*)/", ArtifactHandler),
+            (r"/qiita_db/prep_template/(.*)/data/", PrepTemplateDataHandler),
             (r"/qiita_db/references/(.*)/filepaths/",
              ReferenceFilepathsHandler)
         ]