Labman minimal changes

qiita_db/handlers/sample_information.py

@@ -0,0 +1,34 @@
+# -----------------------------------------------------------------------------
+# 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.
+# -----------------------------------------------------------------------------
+
+import qiita_db as qdb
+from .oauth2 import OauthBaseHandler, authenticate_oauth
+from .util import _get_instance
+
+
+class SampleInfoDBHandler(OauthBaseHandler):
+    @authenticate_oauth
+    def get(self, study_id):
+        """Retrieves the sample information content
+
+        Parameters
+        ----------
+        study_id: str
+            The id of the study whose sample information is being retrieved
+
+        Returns
+        -------
+        dict
+            The contents of the sample information keyed by sample id
+        """
+        with qdb.sql_connection.TRN:
+            ST = qdb.metadata_template.sample_template.SampleTemplate
+            st = _get_instance(ST, study_id, 'Error instantiating sample info')
+            response = {'data': st.to_dataframe().to_dict(orient='index')}
+
+            self.write(response)

qiita_db/handlers/tests/test_sample_information.py

@@ -0,0 +1,72 @@
+# -----------------------------------------------------------------------------
+# 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
+from json import loads
+
+from qiita_db.handlers.tests.oauthbase import OauthTestingBase
+
+
+class SampleInfoDBHandlerTests(OauthTestingBase):
+    def test_get_does_not_exist(self):
+        obs = self.get('/qiita_db/sample_information/100/data/',
+                       headers=self.header)
+        self.assertEqual(obs.code, 404)
+
+    def test_get_no_header(self):
+        obs = self.get('/qiita_db/sample_information/100/data/')
+        self.assertEqual(obs.code, 400)
+
+    def test_get(self):
+        obs = self.get('/qiita_db/sample_information/1/data/',
+                       headers=self.header)
+        self.assertEqual(obs.code, 200)
+
+        obs = loads(obs.body)
+        self.assertEqual(obs.keys(), ['data'])
+
+        # for simplicity we will only test that the keys are the same
+        # and that one of the key's info is correct
+        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 = {'qiita_study_id': '1', 'physical_specimen_location': 'ANL',
+               'tot_org_carb': '5', 'common_name': 'soil metagenome',
+               'water_content_soil': '0.164',
+               'env_feature': 'ENVO:plant-associated habitat',
+               'assigned_from_geo': 'n', 'altitude': '0',
+               'env_biome': ('ENVO:Temperate grasslands, savannas, and '
+                             'shrubland biome'),
+               'texture': '64.6 sand, 17.6 silt, 17.8 clay',
+               'scientific_name': '1118232',
+               'description_duplicate': 'Burmese bulk',
+               'latitude': '4.59216095574', 'ph': '6.94', 'host_taxid': '3483',
+               'elevation': '114', 'description': 'Cannabis Soil Microbiome',
+               'collection_timestamp': '2011-11-11 13:00:00',
+               'physical_specimen_remaining': 'true', 'dna_extracted': 'true',
+               'taxon_id': '410658', 'samp_salinity': '7.15',
+               'host_subject_id': '1001:M2', 'sample_type': 'ENVO:soil',
+               'season_environment': 'winter', 'temp': '15',
+               'country': 'GAZ:United States of America',
+               'longitude': '63.5115213108', 'tot_nitro': '1.41',
+               'depth': '0.15', 'anonymized_name': 'SKB1'}
+        self.assertEqual(obs, exp)
+
+
+if __name__ == '__main__':
+    main()

qiita_db/handlers/tests/test_user.py

@@ -0,0 +1,42 @@
+# -----------------------------------------------------------------------------
+# 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
+from json import loads
+
+from qiita_db.handlers.tests.oauthbase import OauthTestingBase
+
+
+class UserInfoDBHandlerTests(OauthTestingBase):
+    def test_get_does_not_exist(self):
+        obs = self.get('/qiita_db/user/no-exists@foo.bar/data/',
+                       headers=self.header)
+        self.assertEqual(obs.code, 404)
+
+    def test_get_no_header(self):
+        obs = self.get('/qiita_db/user/no-exists@foo.bar/data/')
+        self.assertEqual(obs.code, 400)
+
+    def test_get(self):
+        obs = self.get('/qiita_db/user/shared@foo.bar/data/',
+                       headers=self.header)
+        self.assertEqual(obs.code, 200)
+
+        obs = loads(obs.body)
+        self.assertEqual(obs.keys(), ['data'])
+
+        # for simplicity we will only test that the keys are the same
+        # and that one of the key's info is correct
+        obs = obs['data']
+        exp = {"password": "$2a$12$gnUi8Qg.0tvW243v889BhOBhWLIHyIJjjgaG6dxuRJk"
+               "UM8nXG9Efe", "email": "shared@foo.bar", "level": "user"}
+        self.assertEqual(obs, exp)
+
+
+if __name__ == '__main__':
+    main()

qiita_db/handlers/tests/test_util.py

@@ -0,0 +1,40 @@
+# -----------------------------------------------------------------------------
+# 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
+
+from tornado.web import HTTPError
+
+from qiita_db.handlers.tests.oauthbase import OauthTestingBase
+import qiita_db as qdb
+
+
+class UtilTests(OauthTestingBase):
+    def test_get_sample_info(self):
+        ST = qdb.metadata_template.sample_template.SampleTemplate
+        exp = ST(1)
+        obs = qdb.handlers.util._get_instance(ST, 1, 'error')
+        self.assertEqual(obs, exp)
+
+        # It does not exist
+        with self.assertRaises(HTTPError):
+            qdb.handlers.util._get_instance(ST, 100, 'error')
+
+    def test_get_user_info(self):
+        US = qdb.user.User
+        obs = qdb.handlers.util._get_instance(US, 'shared@foo.bar', 'error')
+        exp = US('shared@foo.bar')
+        self.assertEqual(obs, exp)
+
+        # It does not exist
+        with self.assertRaises(HTTPError):
+            qdb.handlers.util._get_instance(US, 'no-exists@foo.bar', 'error')
+
+
+if __name__ == '__main__':
+    main()

qiita_db/handlers/user.py

@@ -0,0 +1,35 @@
+# -----------------------------------------------------------------------------
+# 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.
+# -----------------------------------------------------------------------------
+
+import qiita_db as qdb
+from .oauth2 import OauthBaseHandler, authenticate_oauth
+from .util import _get_instance
+
+
+class UserInfoDBHandler(OauthBaseHandler):
+    @authenticate_oauth
+    def get(self, email):
+        """Retrieves the User information
+
+        Parameters
+        ----------
+        email: str
+            The email of the user whose information is being retrieved
+
+        Returns
+        -------
+        dict
+            The user information as a dict
+        """
+        with qdb.sql_connection.TRN:
+            user = _get_instance(qdb.user.User, email,
+                                 'Error instantiating user')
+            response = {'data': {'email': email, 'level': user.level,
+                                 'password': user.password}}
+
+            self.write(response)

qiita_db/handlers/util.py

@@ -0,0 +1,45 @@
+# -----------------------------------------------------------------------------
+# 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
+
+
+def _get_instance(klass, oid, reason):
+    """
+    Returns the klass instance with the given `oid`
+
+    Parameters
+    ----------
+    klass : class name
+        The class name to instanciate
+    oid : int/str
+        The object id
+    reason : str
+        The failure reason we want to be displayed
+
+    Returns
+    -------
+    qiita_db.user.User
+        The requested user
+
+    Raises
+    ------
+    HTTPError
+        If the user does not exist, with error code 404
+        If there is a problem instantiating, with error code 500
+    """
+    try:
+        object = klass(oid)
+    except qdb.exceptions.QiitaDBUnknownIDError:
+        raise HTTPError(404)
+    except Exception as e:
+        raise HTTPError(500, reason=reason + ', id=%s: %s' % (oid, str(e)))
+
+    return object

qiita_db/test/test_user.py

@@ -327,10 +327,13 @@ def test_verify_code(self):
         self.assertEqual(self.conn_handler.execute_fetchone(sql)[0], 2)
 
     def _check_pass(self, user, passwd):
-        obspass = self.conn_handler.execute_fetchone(
-            "SELECT password FROM qiita.qiita_user WHERE email = %s",
-            (user.id, ))[0]
-        self.assertEqual(qdb.util.hash_password(passwd, obspass), obspass)
+        self.assertEqual(qdb.util.hash_password(passwd, user.password),
+                         user.password)
+
+    def test_password(self):
+        user = qdb.user.User('shared@foo.bar')
+        self.assertEqual(user.password, '$2a$12$gnUi8Qg.0tvW243v889BhOBhWLIHy'
+                         'IJjjgaG6dxuRJkUM8nXG9Efe')
 
     def test_change_pass(self):
         user = qdb.user.User.create('testchangepass@test.bar', 'password')

qiita_db/user.py

@@ -339,6 +339,17 @@ def email(self):
         """The email of the user"""
         return self._id
 
+    @property
+    def password(self):
+        """The password of the user"""
+        with qdb.sql_connection.TRN:
+            # pull password out of database
+            sql = "SELECT password FROM qiita.{0} WHERE email = %s".format(
+                self._table)
+            qdb.sql_connection.TRN.add(sql, [self.email])
+
+            return qdb.sql_connection.TRN.execute_fetchlast()
+
     @property
     def level(self):
         """The level of privileges of the user"""

qiita_pet/support_files/doc/source/dev/rest.rst

@@ -43,9 +43,13 @@ the important parts of the values are described in the Parameters column.
 |PATCH   | ``/qiita_db/artifacts/<artifact_id>/``                                            | ``op: operation``, ``path: path``,      | Retrieves the artifact information                  | ArtifactHandler            |
 |        |                                                                                   | ``value: value``                        |                                                     |                            |
 +--------+-----------------------------------------------------------------------------------+-----------------------------------------+-----------------------------------------------------+----------------------------+
+|GET     | ``/qiita_db/user/<email>/data/``                                                  |                                         | Retrieves the user information                      | UserInfoDBHandlerTests     |
++--------+-----------------------------------------------------------------------------------+-----------------------------------------+-----------------------------------------------------+----------------------------+
+|GET     | ``/qiita_db/sample_information/<study_id>/data/``                                 |                                         | Retrieves the sample information contents           | SampleInfoDBHandler        |
++--------+-----------------------------------------------------------------------------------+-----------------------------------------+-----------------------------------------------------+----------------------------+
 |GET     | ``/qiita_db/prep_template/<prep_id>/data/``                                       |                                         | Retrieves the preparation information contents      | PrepTemplateDataHandler    |
 +--------+-----------------------------------------------------------------------------------+-----------------------------------------+-----------------------------------------------------+----------------------------+
-|GET     | ``/qiita_db/prep_template/<prep_id>/``                                            |                                         | Retrieves the preparation template information      | PrepTemplateDBHandler      |
+|GET     | ``/qiita_db/prep_template/<prep_id>/``                                            |                                         | Retrieves the preparation information               | PrepTemplateDBHandler      |
 +--------+-----------------------------------------------------------------------------------+-----------------------------------------+-----------------------------------------------------+----------------------------+
 |GET     | ``/qiita_db/plugins/<plugin_name>/<version>/commands/<command_name>/activate/``   |                                         | Activates the command                               | CommandActivateHandler     |
 +--------+-----------------------------------------------------------------------------------+-----------------------------------------+-----------------------------------------------------+----------------------------+

qiita_pet/webserver.py

@@ -58,6 +58,8 @@
     ProcessingJobAPItestHandler)
 from qiita_db.handlers.artifact import (
     ArtifactHandler, ArtifactAPItestHandler, ArtifactTypeHandler)
+from qiita_db.handlers.sample_information import SampleInfoDBHandler
+from qiita_db.handlers.user import UserInfoDBHandler
 from qiita_db.handlers.prep_template import (
     PrepTemplateDataHandler, PrepTemplateAPItestHandler,
     PrepTemplateDBHandler)
@@ -192,6 +194,8 @@ def __init__(self):
             (r"/qiita_db/jobs/(.*)", JobHandler),
             (r"/qiita_db/artifacts/types/", ArtifactTypeHandler),
             (r"/qiita_db/artifacts/(.*)/", ArtifactHandler),
+            (r"/qiita_db/user/(.*)/data/", UserInfoDBHandler),
+            (r"/qiita_db/sample_information/(.*)/data/", SampleInfoDBHandler),
             (r"/qiita_db/prep_template/(.*)/data/", PrepTemplateDataHandler),
             (r"/qiita_db/prep_template/(.*)/", PrepTemplateDBHandler),
             (r"/qiita_db/references/(.*)/", ReferenceHandler),