Upstream master 0502018

.travis.yml

@@ -4,7 +4,7 @@ sudo: false
 env:
   global:
     - PYTHON_VERSION=3.5
-    - secure: "bR44P87PdbaXtdh4SMw7wF6pVCvPF1UkJequCABT1fQknljI2seBLda6otdXFJiWynmvKnubJQh2iz22wJ/maLwhoNorZ7OLFof0pRtA916uoBzcWCeocf1QhPxqR2kJOIV4oaRSdd9xvy9oKS3lrODxyuQ2CTnWMYD9oe9n8qk="
+    - secure: "OFyFddp26BbuaYxD2suftmbSfyaLcvleOL9heGh4IqqbvDVX+EcaqvmUALRaBL4HQlK5W0rO9H4pFsXuq26Xl3S2EKr+Pne4SDlw9ekmU3n6bWVNwReG7V+9c7OEgfNHbZ4pNwRzti62n1ESlRSZVkLVGg+pI0Ikvbh1+yUm9Eg="
   matrix:
     - TEST_ADD_STUDIES=False COVER_PACKAGE=qiita_db
     - TEST_ADD_STUDIES=False COVER_PACKAGE=qiita_pet

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

@@ -54,12 +54,19 @@ Rarefying Features
 .. figure::  rarefy.png
    :align:   center
 
-* **Rarefy features** :ref:`[11]<reference11>` , :ref:`[12]<reference12>` : Subsample frequencies from all samples without replacement so that the sum of frequencies in each sample is equal to the sampling-depth
+* **Rarefy features**: Subsample frequencies from all samples without replacement so that the sum of frequencies in each sample is equal to the sampling-depth.
 
   *  **BIOM table** (required): Feature table containing the samples for which features should be rarefied
   *  **Parameter set**: Parameters at which the rarefication is run
   *  **Sampling depth** (required): Total frequency that each sample should be rarefied to, samples where sum of frequencies is less than sampling depth will not be included in resulting table
 
+Note that rarefaction has some advantages for beta-diversity analyses
+:ref:`[11]<reference11>`, but can have undesirable properties in tests of
+differential abundance :ref:`[12]<reference12>`. To analyze your data with
+alternative normalization strategies, you can easily download the raw biom
+tables (see :doc:`../tutorials/downloading`) and load them into an analysis
+pipeline such as `Phyloseq <https://bioconductor.org/packages/release/bioc/html/phyloseq.html>`__.
+
 Filtering Samples by Metadata
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 
@@ -369,9 +376,6 @@ Calculating Beta Group Significance
 .. figure::  beta_group_significance.png
    :align:   center
 
-Calculating Beta Group Significance
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-
 * **Calculate beta group significance**: Determines whether groups of samples are significantly different from one another using a permutation-based statistical test
 
   * **Distance matrix** (required): Matrix of distances between pairs of samples
@@ -384,12 +388,12 @@ Calculating Beta Group Significance
 
   * **Number of permutations** (required): Number of permutations to be run when computing p-values
 
-.. figure::  beta_correlation.png
-   :align:   center
-
 Calculating Beta Correlation
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 
+.. figure::  beta_correlation.png
+   :align:   center
+
 * **Calculate beta correlation**: Identifies a correlation between the distance matrix and a numeric sample metadata category
 
   * **Distance-matrix** (required): Matrix of distances between pairs of samples

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

@@ -89,8 +89,8 @@ EBI-ENA NULL values vocabulary
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 
 For all public studies including those being submitted to EBI, no blanks are allowed in the sample information.
-We support the following null values: *not applicable*, *missing: not collected*, *missing: not provided*,
-*missing: restricted access*.
+We support the following null values: *not applicable*, *not collected*, *not provided*,
+*restricted access*.
 
 For the latest definitions and explanation visit the `EBI/ENA Missing value reporting <http://www.ebi.ac.uk/ena/about/missing-values-reporting>`__.
 

qiita_pet/templates/artifact_ajax/artifact_summary.html

@@ -159,9 +159,10 @@ <h4>
 {% if files %}
 <div class='row'>
   <div class='col-md-12'>
+    <b>Available files:</b>
     <button class="btn btn-default" data-toggle="collapse" data-target="#available-files-div">
       <span class="glyphicon glyphicon-eye-open"></span>
-      Available files:
+      Show/Hide
     </button>
     <div id="available-files-div" class="collapse {% if len(files) <= 10 %} in {% end %}" style="padding: 10px 10px 10px 10px; border-radius: 10px; background: #EEE;">
       {% for f_id, f_name in files %}

qiita_ware/test/test_commands.py

@@ -13,12 +13,14 @@
 from tempfile import mkdtemp
 import pandas as pd
 from datetime import datetime
+from shutil import rmtree
 
 from h5py import File
 from qiita_files.demux import to_hdf5
 
-from qiita_ware.exceptions import ComputeError, EBISubmissionError
+from qiita_ware.exceptions import ComputeError
 from qiita_ware.commands import submit_EBI
+from qiita_db.util import get_mountpoint
 from qiita_db.study import Study, StudyPerson
 from qiita_db.software import DefaultParameters, Parameters
 from qiita_db.artifact import Artifact
@@ -34,6 +36,7 @@ def setUp(self):
         self.files_to_remove = []
         self.temp_dir = mkdtemp()
         self.files_to_remove.append(self.temp_dir)
+        _, self.base_fp = get_mountpoint("preprocessed_data")[0]
 
     def write_demux_files(self, prep_template, generate_hdf5=True):
         """Writes a demux test file to avoid duplication of code"""
@@ -135,33 +138,40 @@ def generate_new_study_with_preprocessed_data(self):
         return ppd
 
     def test_submit_EBI_step_2_failure(self):
-        ppd = self.write_demux_files(PrepTemplate(1), False)
+        ppd = self.write_demux_files(PrepTemplate(1), True)
+        pid = ppd.id
 
-        with self.assertRaises(EBISubmissionError):
-            submit_EBI(ppd.id, 'VALIDATE', True)
+        with self.assertRaises(ComputeError):
+            submit_EBI(pid, 'VALIDATE', True)
+
+        rmtree(join(self.base_fp, '%d_ebi_submission' % pid), True)
 
     @skipIf(
         environ.get('ASPERA_SCP_PASS', '') == '', 'skip: ascp not configured')
     def test_submit_EBI_parse_EBI_reply_failure(self):
         ppd = self.write_demux_files(PrepTemplate(1))
+        pid = ppd.id
 
         with self.assertRaises(ComputeError) as error:
-            submit_EBI(ppd.id, 'VALIDATE', True)
+            submit_EBI(pid, 'VALIDATE', True)
         error = str(error.exception)
         self.assertIn('EBI Submission failed! Log id:', error)
         self.assertIn('The EBI submission failed:', error)
-        self.assertIn(
-            'Failed to validate run xml, error: Expected element', error)
+
+        rmtree(join(self.base_fp, '%d_ebi_submission' % pid), True)
 
     @skipIf(
         environ.get('ASPERA_SCP_PASS', '') == '', 'skip: ascp not configured')
     def test_full_submission(self):
         artifact = self.generate_new_study_with_preprocessed_data()
         self.assertEqual(
             artifact.study.ebi_submission_status, 'not submitted')
-        submit_EBI(artifact.id, 'VALIDATE', True, test=True)
+        aid = artifact.id
+        submit_EBI(aid, 'VALIDATE', True, test=True)
         self.assertEqual(artifact.study.ebi_submission_status, 'submitted')
 
+        rmtree(join(self.base_fp, '%d_ebi_submission' % aid), True)
+
 
 FASTA_EXAMPLE = """>1.SKB2.640194_1 X orig_bc=X new_bc=X bc_diffs=0
 CCACCCAGTAAC