update: enlarge client body size of nginx

nginx/production/taibif.conf

@@ -21,6 +21,7 @@ server {
     charset utf-8;
     server_name portal.taibif.tw;
     server_tokens off;
+    client_max_body_size  100M;
 
     location /.well-known/acme-challenge/ {
       root /var/www/certbot;
@@ -35,6 +36,7 @@ server {
     charset utf-8;
     server_name portal.taibif.tw;
     server_tokens off;
+    client_max_body_size  100M;
 
     ssl_certificate /etc/letsencrypt/live/portal.taibif.tw/fullchain.pem;
     ssl_certificate_key /etc/letsencrypt/live/portal.taibif.tw/privkey.pem;

taxon_mapping/gbif_taxon.py

@@ -6,11 +6,13 @@
 from datetime import date
 
 def update_namecode(row):
-    gbif_url = 'http://127.0.0.1:8080/v2/api.php?format=json&source=gbif_backbone_txn&best=yes&names=' + str(row['name'])
+    gbif_url = 'http://127.0.0.1:8081/api.php?format=json&source=gbif_backbone_txn&best=yes&names=' + str(row['name'])
 
     # solr 呼叫 nomanmatch 查詢
-    gbif_response = requests.post(gbif_url, json={"test": "in"})
-    gbif_data = json.loads(gbif_response.content.decode('utf-8'))
+    # gbif_response = requests.post(gbif_url, json={"test": "in"})
+    # gbif_data = json.loads(gbif_response.content.decode('utf-8'))
+    gbif_response = requests.get(gbif_url)
+    gbif_data = gbif_response.json()
 
     try:
         if gbif_data['data'][0][0]['results'][0]['match_type'] == 'Full match':
@@ -22,9 +24,11 @@ def update_namecode(row):
 
 
 def check_namecode(row):
-    taicol_url = 'http://127.0.0.1:8080/v2/api.php?format=json&source=taicol&best=yes&names=' + str(row['nM_name'])
-    taicol_response = requests.post(taicol_url, json={"test": "in"})
-    taicol_data = json.loads(taicol_response.content.decode('utf-8'))
+    taicol_url = 'http://127.0.0.1:8081/api.php?format=json&source=taicol&best=yes&names=' + str(row['nM_name'])
+    # taicol_response = requests.post(taicol_url, json={"test": "in"})
+    # taicol_data = json.loads(taicol_response.content.decode('utf-8'))
+    taicol_response = requests.get(taicol_url)
+    taicol_data = taicol_response.json()
 
 
     # taicol_data 無資料會報錯後去查詢GBIF
@@ -33,9 +37,12 @@ def check_namecode(row):
             row['taxon_backbone'] = 'TaiCOL'
     except:
 
-        gbif_url = 'http://127.0.0.1:8080/v2/api.php?format=json&source=gbif_backbone_txn&best=yes&names='+str(row['nM_name'])
-        gbif_response = requests.post(gbif_url, json={"test": "in"})
-        gbif_data = json.loads(gbif_response.content.decode('utf-8'))
+        gbif_url = 'http://127.0.0.1:8080/api.php?format=json&source=gbif_backbone_txn&best=yes&names='+str(row['nM_name'])
+        # gbif_response = requests.post(gbif_url, json={"test": "in"})
+        # gbif_data = json.loads(gbif_response.content.decode('utf-8'))
+
+        gbif_response = requests.get(gbif_url)
+        gbif_data = gbif_response.json()
 
         try:
             if gbif_data['data'][0][0]['results'][0]['match_type'] == 'Full match':
@@ -122,7 +129,7 @@ def check_namecode(row):
 
 tmp_nomenMatch_result = taxon_file.apply(update_namecode, axis=1)
 
-# 合併specie 資訊
+# 合併species 資訊
 seperated_file = seperated_file.rename(columns={'taibif_scientificname':'name','taxon_backbone':'backbone','taxon_rank':'rank'})
 seperated_file = seperated_file.drop(columns=['Unnamed: 0','nM_name','taibif_vernacular_name','kingdomzh','phylumzh','classzh','orderzh','familyzh','genuszh'])
 # print('seperated_file == ',seperated_file)

taxon_mapping/main.py

@@ -160,21 +160,21 @@ def update_highertaxon_api(row):
     return pd.Series(row) 
 
 
-# 前置準備 - 建立 Postgres 資料庫於本地端，目前設置port為 9432
+# 前置準備 - 建立 Postgres 資料庫於本地端，目前設置port為 5432
 
 # 1. 原本 TaiCOL 更新
 # 2. 新 TaiCOL 加入
 
 print("==== STEP 0 = Load Database Information ====")
 
-engine = db.create_engine('postgresql://postgres:[email protected]:9432/taibif') 
+engine = db.create_engine('postgresql://postgres:[email protected]:5432/taibif') 
 connection = engine.connect()
 df_taxon = pd.read_sql('SELECT * FROM data_taxon', connection)
 
 # ---- update Taxon information 
-sql_delete_temp_taxon =  "DELETE FROM temp_taxon"
-with engine.begin() as conn:    
-    conn.execute(sql_delete_temp_taxon)
+# sql_delete_temp_taxon =  "DELETE FROM temp_taxon"
+# with engine.begin() as conn:    
+#     conn.execute(sql_delete_temp_taxon)
 
 df_taxon['mapping_error'] = ''
 df_taicolid_notnull = df_taxon[df_taxon.taicol_taxon_id.notnull()]