Merge pull request #3301 from antgonza/geographic-location

geographic location (country and/or sea)

Author: charles-cowart

qiita_pet/support_files/doc/source/checklist-for-ebi-ena-submission.rst

@@ -76,8 +76,15 @@ Remember, metadata is the most important part for an analysis, without it we onl
       6. *env_biome*, *env_feature*, *env_material*, *env_package*, for options `visit ENVO <http://ols.wordvis.com/>`__
       7. *elevation*, *latitude*, *longitude*
       8. *physical_specimen_location*
-      9. *collection_timestamp*
-      10. *empo_1*, *empo_2*, *empo_3*, *empo_4*, more info: :ref:`empo`
+      9. *collection_date*
+      10. *country*
+
+          .. note::
+             The EBI-ENA submission requires to have a *geographic location (country and/or sea)*
+             so during submission Qiita will automatically replace *country* to match that
+             requirement.
+
+      11. *empo_1*, *empo_2*, *empo_3*, *empo_4*, more info: :ref:`empo`
 
          .. table::
             :widths: auto

qiita_ware/commands.py

@@ -229,7 +229,8 @@ def submit_EBI(artifact_id, action, send, test=False, test_size=False):
             nunique[(nunique <= int(nsamples * .01)) |
                     (nunique >= int(nsamples * .5))].index)
         cols_to_drop = cols_to_drop - {'taxon_id', 'scientific_name',
-                                       'description'}
+                                       'description', 'country',
+                                       'collection_date'}
         all_samples = ebi_submission.sample_template.ebi_sample_accessions
         samples = [k for k in ebi_submission.samples if all_samples[k] is None]
         if samples:

qiita_ware/ebi.py

@@ -402,6 +402,9 @@ def generate_sample_xml(self, samples=None, ignore_columns=None):
 
         for sample_name in sorted(samples):
             sample_info = dict(self.samples[sample_name])
+            if 'country' in sample_info.keys():
+                nname = 'geographic location (country and/or sea)'
+                sample_info[nname] = sample_info['country']
 
             sample_accession = self._ebi_sample_accessions[sample_name]
             if self.action in ('ADD', 'VALIDATE'):