minor fixes from latests ENA and SPP changes (#3472)

Author: antgonza

.gitignore

@@ -75,3 +75,6 @@ notebooks/*/*.tsv.gz
 
 # jupyter notebooks input data
 notebooks/resource-allocation/data
+
+# ignore plugin SQL injection file
+qiita_db/support_files/patches/test_db_sql/91.sql

qiita_pet/handlers/study_handlers/prep_template.py

@@ -77,18 +77,22 @@ def get(self):
         res['alert_message'] = url_escape(res['alert_message'])
         res['user_level'] = current_user.level
         if res['creation_job'] is not None:
-            fp = res['creation_job'].parameters.values['sample_sheet']
-            res['creation_job_filename'] = fp['filename']
-            res['creation_job_filename_body'] = fp['body']
+            params = res['creation_job'].parameters.values
             summary = None
-            if res['creation_job'].status == 'success':
-                if res['creation_job'].outputs:
-                    # [0] is the id, [1] is the filepath
-                    _file = res['creation_job'].outputs[
-                        'output'].html_summary_fp[1]
-                    summary = relpath(_file, qiita_config.base_data_dir)
+            if 'sample_sheet' in params:
+                fp = params['sample_sheet']
+                res['creation_job_filename'] = fp['filename']
+                res['creation_job_filename_body'] = fp['body']
+                if res['creation_job'].status == 'success':
+                    if res['creation_job'].outputs:
+                        # [0] is the id, [1] is the filepath
+                        _file = res['creation_job'].outputs[
+                            'output'].html_summary_fp[1]
+                        summary = relpath(_file, qiita_config.base_data_dir)
+            else:
+                res['creation_job_filename'] = None
+                res['creation_job_filename_body'] = None
             res['creation_job_artifact_summary'] = summary
-        # res['']
         res['human_reads_filter_method'] = None
         a = PrepTemplate(prep_id).artifact
         if a is not None:

qiita_ware/ebi.py

@@ -33,6 +33,12 @@
 from qiita_db.processing_job import _system_call as system_call
 
 
+ENA_COLS_TO_FIX = {
+    'country': 'geographic location (country and/or sea)',
+    'collection_date': 'collection date'
+}
+
+
 def clean_whitespace(text):
     """Standardizes whitespaces so there is only one space separating tokens
 
@@ -407,9 +413,9 @@ 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']
+            for qname, ename in ENA_COLS_TO_FIX.items():
+                if qname in sample_info.keys():
+                    sample_info[ename] = sample_info[qname]
 
             sample_accession = self._ebi_sample_accessions[sample_name]
             if self.action in ('ADD', 'VALIDATE'):