Fix #3149

qiita_db/handlers/studies.py

@@ -0,0 +1,67 @@
+# -----------------------------------------------------------------------------
+# 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
+
+from qiita_db.sql_connection import TRN
+from .oauth2 import OauthBaseHandler, authenticate_oauth
+
+
+def _generate_study_list_for_api(visibility, only_biom=True):
+    """Get general study information
+
+    Parameters
+    ----------
+    visibility : string
+        The visibility to get studies
+
+    Returns
+    -------
+    list of dict
+        The list of studies and their information
+    """
+    artifact_type = ''
+    if only_biom:
+        artifact_type = "AND artifact_type = 'BIOM'"
+
+    sql = f"""
+        SELECT study_id, array_agg(DISTINCT artifact_id) FROM qiita.study
+            INNER JOIN qiita.study_artifact USING (study_id)
+            INNER JOIN qiita.artifact USING (artifact_id)
+            INNER JOIN qiita.artifact_type USING (artifact_type_id)
+            INNER JOIN qiita.visibility USING (visibility_id)
+        WHERE visibility = %s
+        {artifact_type}
+        GROUP BY study_id
+    """
+    with TRN:
+        TRN.add(sql, [visibility])
+        return dict(TRN.execute_fetchindex())
+
+
+class APIStudiesListing(OauthBaseHandler):
+    @authenticate_oauth
+    def get(self, visibility):
+        """Retrieves the studies and their BIOM artifacts in visibility
+
+        Parameters
+        ----------
+        visibility : str {'public', 'sandbox'}
+            The visibility of the studies and artifacts requested
+
+        Returns
+        -------
+        see qiita_db.util.generate_study_list
+        """
+        if visibility not in {'public', 'private'}:
+            raise HTTPError(
+                403, reason='You can only request public or private studies')
+
+        response = {
+            'data': _generate_study_list_for_api(visibility=visibility)}
+        self.write(response)

qiita_db/handlers/tests/test_studies.py

@@ -0,0 +1,37 @@
+# -----------------------------------------------------------------------------
+# 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 TestAPIStudiesListing(OauthTestingBase):
+    def setUp(self):
+        super(TestAPIStudiesListing, self).setUp()
+
+    def test_get_studies_failure(self):
+        obs = self.get('/qiita_db/studies/not-valid', headers=self.header)
+        self.assertEqual(obs.code, 403)
+        self.assertEqual(str(obs.error), 'HTTP 403: You can only request '
+                         'public or private studies')
+
+    def test_get_studies_private(self):
+        obs = self.get('/qiita_db/studies/private', headers=self.header)
+        exp = {'data': {'1': [4, 5, 6, 7]}}
+        self.assertEqual(loads(obs.body), exp)
+
+    def test_get_studies_public(self):
+        obs = self.get('/qiita_db/studies/public', headers=self.header)
+        exp = {'data': {}}
+        self.assertEqual(loads(obs.body), exp)
+
+
+if __name__ == '__main__':
+    main()

qiita_pet/handlers/rest/study_samples.py

@@ -6,6 +6,8 @@
 # The full license is in the file LICENSE, distributed with this software.
 # -----------------------------------------------------------------------------
 from collections import defaultdict
+import io
+from qiita_db.metadata_template.util import load_template_to_dataframe
 
 from tornado.escape import json_encode, json_decode
 import pandas as pd
@@ -150,13 +152,20 @@ def patch(self, study_id):
         else:
             sample_info = study.sample_template.to_dataframe()
 
-        data = pd.DataFrame.from_dict(json_decode(self.request.body),
-                                      orient='index')
-
-        if len(data.index) == 0:
+        # convert from json into a format that qiita can validate
+        rawdata = pd.DataFrame.from_dict(json_decode(self.request.body),
+                                         orient='index')
+        rawdata.index.name = 'sample_name'
+        if len(rawdata.index) == 0:
             self.fail('No samples provided', 400)
             return
 
+        buffer = io.StringIO()
+        rawdata.to_csv(buffer, sep='\t', index=True, header=True)
+        buffer.seek(0)
+        # validate on load
+        data = load_template_to_dataframe(buffer)
+
         categories = set(study.sample_template.categories)
 
         if set(data.columns) != categories:

qiita_pet/support_files/doc/source/processingdata/index.rst

@@ -115,13 +115,13 @@ Deblurring
   * **Input Data** (required): Data being trimmed
   * **Parameter Set** (required): How many bases to trim off
 
-    * **90 base pairs**- Removes first 90 base pairs from the sequences
-    * **100 base pairs**- Removes first 100 base pairs from the sequences
-    * **125 base pairs**- Removes first 125 base pairs from the sequences
-    * **150 base pairs**- Removes first 150 base pairs from the sequences
-    * **200 base pairs**- Removes first 200 base pairs from the sequences
-    * **250 base pairs**- Removes first 250 base pairs from the sequences
-    * **300 base pairs**- Removes first 300 base pairs from the sequences
+    * **90 base pairs**- Keeps first 90 base pairs from the sequences
+    * **100 base pairs**- Keeps first 100 base pairs from the sequences
+    * **125 base pairs**- Keeps first 125 base pairs from the sequences
+    * **150 base pairs**- Keeps first 150 base pairs from the sequences
+    * **200 base pairs**- Keeps first 200 base pairs from the sequences
+    * **250 base pairs**- Keeps first 250 base pairs from the sequences
+    * **300 base pairs**- Keeps first 300 base pairs from the sequences
 
 **Command from Trimmed Artifact**:
 

qiita_pet/webserver.py

@@ -78,6 +78,7 @@
     ReloadPluginAPItestHandler)
 from qiita_db.handlers.analysis import APIAnalysisMetadataHandler
 from qiita_db.handlers.archive import APIArchiveObservations
+from qiita_db.handlers.studies import APIStudiesListing
 from qiita_db.util import get_mountpoint
 from qiita_pet.handlers.rest import ENDPOINTS as REST_ENDPOINTS
 from qiita_pet.handlers.qiita_redbiom import RedbiomPublicSearch
@@ -229,7 +230,8 @@ def __init__(self):
             (r"/qiita_db/plugins/(.*)/(.*)/commands/", CommandListHandler),
             (r"/qiita_db/plugins/(.*)/(.*)/", PluginHandler),
             (r"/qiita_db/analysis/(.*)/metadata/", APIAnalysisMetadataHandler),
-            (r"/qiita_db/archive/observations/", APIArchiveObservations)
+            (r"/qiita_db/archive/observations/", APIArchiveObservations),
+            (r"/qiita_db/studies/(.*)", APIStudiesListing)
         ]
 
         # rest endpoints