# HG changeset patch
# User ieguinoa
# Date 1605536699 0
# Node ID 6c82d674873b9077985938fc1f587e9fb3ec6db7
# Parent  fb51bbda07d73781c006789eb732d0737c0071be
Uploaded

diff -r fb51bbda07d7 -r 6c82d674873b ena_upload.xml
--- a/ena_upload.xml	Tue Nov 10 21:35:20 2020 +0000
+++ b/ena_upload.xml	Mon Nov 16 14:24:59 2020 +0000
@@ -10,12 +10,13 @@
   <command detect_errors="exit_code"><![CDATA[
 cwd=\$(pwd);
 #set $use_secret = "False"
-#set $webin_id = $__user__.extra_preferences.get('ena_account|webin_id', "")
-#set $password = $__user__.extra_preferences.get('ena_account|password', "")
+#set $webin_id = $__user__.extra_preferences.get('ena_account|webin_id', "").strip()
+#set $password = $__user__.extra_preferences.get('ena_account|password', "").strip()
+echo $webin_id;
 #if $webin_id == "":
     ## No user defined credentials, try with global webin_id + secret file path
-    #set webin_id = os.environ.get('WEBIN_ID', "")
-    #set webin_secret = os.environ.get('WEBIN_SECRET', None)
+    #set webin_id = os.environ.get('WEBIN_ID', "").strip()
+    #set webin_secret = os.environ.get('WEBIN_SECRET', "").strip()
     #set use_secret = "True"
     #if webin_id == "":
         echo "No ENA credentials defined. Set your credentials via: User -> Preferences -> Manage Information";
diff -r fb51bbda07d7 -r 6c82d674873b process_xlsx.py
--- a/process_xlsx.py	Tue Nov 10 21:35:20 2020 +0000
+++ b/process_xlsx.py	Mon Nov 16 14:24:59 2020 +0000
@@ -62,7 +62,7 @@
 if(xl_sheet.nrows < 3):
     raise ValueError('No entries found in samples')
 if args.viral_submission:
-    samples_cols = ['alias','title','scientific_name','sample_description','collection date','geographic location (country and/or sea)', 'geographic location (region and locality)', 'sample capture status', 'host disease outcome', 'host common name', 'host age', 'host health state', 'host sex', 'host scientific name', 'virus identifier', 'collector name', 'collecting institution', 'isolate','isolation source host-associated']
+    samples_cols = ['alias','title','scientific_name','sample_description','geographic location (country and/or sea)', 'host common name', 'host health state', 'host sex', 'host scientific name', 'collector name', 'collection date','collecting institution', 'isolate']
 else:
     samples_cols = ['alias','title','scientific_name','sample_description']
 samples_dict = extract_data(xl_sheet, samples_cols)
@@ -99,7 +99,7 @@
 
 samples_table = open(pathlib.Path(args.out_path) / 'samples.tsv', 'w')
 if args.viral_submission:
-    samples_table.write('\t'.join(['alias','status','accession','title','scientific_name','taxon_id','sample_description','collection_date','geographic_location','host_common_name','host_subject_id','host_health_state','host_sex','host_scientific_name','collector_name','collecting_institution','isolate','submission_date']) + '\n')
+    samples_table.write('\t'.join(['alias','status','accession','title','scientific_name','taxon_id','sample_description','collection date','geographic_location','host_common_name','host_subject_id','host_health_state','host_sex','host_scientific_name','collector_name','collecting_institution','isolate','submission_date']) + '\n')
 else:
     samples_table.write('\t'.join(['alias','status','accession','title','scientific_name','taxon_id','sample_description','submission_date'])+ '\n')