Merge pull request #3152 from qiita-spots/issue-3149

Fix #3149

Author: wasade

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**: