update mirri folder

mirri/io/writers/mirri_excel.py

@@ -50,11 +50,10 @@ PUB_HEADERS = [pb["label"] for pb in PUBLICATION_FIELDS]
 
 
 def write_mirri_excel(path, strains, growth_media, version):
-    if version == "20200601":
-        _write_mirri_excel_20200601(path, strains, growth_media)
+    if version == "5.1.2":
+        _write_mirri_excel_12052023(path, strains, growth_media)
 
-
-def _write_mirri_excel_20200601(path, strains, growth_media):
+def _write_mirri_excel_12052023(path, strains, growth_media):
     wb = Workbook()
 
     write_markers_sheet(wb)
@@ -104,7 +103,7 @@ def _write_mirri_excel_20200601(path, strains, growth_media):
     redimension_cell_width(pub_sheet)
 
     # write sexual states
-    sex_sheet = wb.create_sheet("Sexual states")
+    sex_sheet = wb.create_sheet("Sexual state")
     for sex_state in sorted(list(sexual_states)):
         sex_sheet.append([sex_state])
     redimension_cell_width(sex_sheet)
@@ -121,7 +120,6 @@ def _write_mirri_excel_20200601(path, strains, growth_media):
     del wb["Sheet"]
     wb.save(str(path))
 
-
 def _deserialize_strains(strains, locations, growth_media_indexes,
                          publications, sexual_states, genomic_markers):
     for strain in strains:
@@ -189,10 +187,21 @@ def _deserialize_strains(strains, locations, growth_media_indexes,
             elif attribute == "collect.location.coords":
                 lat = strain.collect.location.latitude
                 long = strain.collect.location.longitude
-                if lat is not None and long is not None:
-                    value = f"{lat};{long}"
+                alt = strain.collect.location.altitude 
+                prec = strain.collect.location.precision
+                if lat is not None and long is not None and prec is not None and alt is not None:
+                    value = f"{lat};{long};{prec};{alt}"
                 else:
-                    value = None
+                    value = None     
+            elif attribute == "collect.site.links":
+                name = strain.collect.site.links.nameSite
+                url = strain.collect.site.links.urlSite
+                value = rgetattr(strain, attribute)
+                value = ";".join(value)
+                if name is not None and url is not None:
+                    value = f"{name};{url}"
+                else:
+                    value = None        
 
             elif attribute == "collect.location":
                 location = strain.collect.location