Buf fix on taxonomy tree

json_taxo.py

@@ -33,7 +33,7 @@ def create_json(cur, taxo_path):
     json_root["state"] = state
 
     # on construit children en ajoutant l'element racine -> taxonId = -1 (root)
-    add_childs(cur, json_root, -1)
+    add_childs(cur, json_root, 89593)
 
     json_array.append(json_root)
     #print(json_array)

postgresql/fill_taxo.py

@@ -24,7 +24,7 @@ def load_file(path):
             print(line)
             insert_data(line)
         
-        add_root()
+        #add_root()
         #re_arrange()
 
 def insert_data(raw):
@@ -33,9 +33,10 @@ def insert_data(raw):
     commonName = raw[1]
     scientificName = raw[2]
     rank = raw[4]
-    if rank=="no rank":
-        parentId=-1
-    else:
+    #if rank=="no rank":
+    #    parentId=-1
+    #else:
+    #    parentId=raw[3]
     parentId = raw[3]
     sql = "INSERT INTO taxonomy(taxonid, commonname, scientificname, parent, rank) VALUES(%s,%s,%s,%s,%s)"
     #print(sql)
@@ -51,7 +52,7 @@ def insert_data(raw):
 def add_root():
     config = load_config()
     insert = "INSERT INTO taxonomy(taxonid, commonname) VALUES(%s,%s)"
-    update = "UPDATE taxonomy set parent=-1 WHERE rank='no_rank'"
+    update = "UPDATE taxonomy set parent=-1 WHERE rank='subphylum'"
     try:
         with  psycopg2.connect(**config) as conn:
             with  conn.cursor() as cur:

taxonomy_reduced.tsv

@@ -234,7 +234,7 @@ Taxon Id	Common name	Scientific name	Parent	Rank
 51338	 	Castor canadensis	10184	species
 9376	 	Soricidae	9362	family
 9900	 	Bison	27592	genus
-89593	 	Craniata	 	subphylum
+89593	 	Craniata	0	subphylum
 41426	 	Phacochoerus africanus	41425	species
 9738	 	Tursiops	9726	genus
 54602	 	Macaca thibetana	9539	species