Bug fixes: Handled 'collection date' error and ENA error when uploadi…

…ng reads manifests
collaborative-open-plant-omics · Nov 30, 2023 · 0eae863 · 0eae863
1 parent ce2901a
commit 0eae863
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Showing 3 changed files with 19 additions and 4 deletions.
diff --git a/web/apps/web_copo/utils/dtol/Dtol_Helpers.py b/web/apps/web_copo/utils/dtol/Dtol_Helpers.py
@@ -80,7 +80,7 @@ def check_taxon_ena_submittable(taxon, by="id"):
                 errors.append("TAXON_ID " + taxon + " is not submittable to ENA")
             if taxinfo[0]["rank"] not in ["species", "subspecies"]:
                 errors.append("TAXON_ID " + taxon + " is not a 'species' or 'subspecies' level entity.")
-            if taxinfo["binomial"] == "false":
+            if taxinfo[0]["binomial"] == "false":
                 errors.append(msg['validation_msg_invalid_binomial_name'] % (taxon, taxinfo["scientificName"]))    
     except Exception as e:
         l.exception(e)

diff --git a/web/apps/web_copo/validators/ena_validators/ena_checklist_validators.py b/web/apps/web_copo/validators/ena_validators/ena_checklist_validators.py
@@ -1,3 +1,4 @@
+from datetime import datetime
 from web.apps.web_copo.validators.validator import Validator
 from web.apps.web_copo.validators.validation_messages import MESSAGES as msg
 from dal.copo_da import Sample 
@@ -53,8 +54,22 @@ def validate(self):
                             regex = field.get("regex","")
                             if regex:
                                 if not re.match(regex, row):
-                                    self.errors.append("Invalid value '" + row + "' in column : '" + field["name"] + "' at row " + str(i))
-                                    self.flag = False
+                                    if column == 'collection date':
+                                        # Remove the time part from the date string if it is present
+                                        try:
+                                            result = bool(datetime.strptime(row, "%Y-%m-%d %H:%M:%S"))
+                                        except ValueError:
+                                               result = False
+
+                                        if result:
+                                            row = row.split(' ')[0]
+                                            self.data.at[i-2, column] = row
+                                        else:
+                                            self.errors.append("Invalid value '" + row + "' in column : '" + field["name"] + "' at row " + str(i))
+                                            self.flag = False
+                                    else:
+                                        self.errors.append("Invalid value '" + row + "' in column : '" + field["name"] + "' at row " + str(i))
+                                        self.flag = False
                         elif type == "TAXON_FIELD":
                             if row not in biosampleAccessionsMap.keys():
                                 self.errors.append("Invalid value " + row + " in column:'" + field["name"] + "'")

diff --git a/web/apps/web_copo/views.py b/web/apps/web_copo/views.py
@@ -787,7 +787,7 @@ def agave_oauth(request):
 
 def import_ena_accession(request):
     if request.method == 'GET':
-        profile_id = request.session['profile_id']
+        profile_id = request.session.get('profile_id','')
         return render(request, 'copo/import_ena_accession.html', {'profile_id': profile_id})
     else:
         accessions = request.POST['accessions']