第一次合并clean代码

clean/step4.2_modify_md_with_database.py

@@ -0,0 +1,51 @@
+import mysql.connector
+import tqdm
+import os
+
+TABLE_NAME = 'phosphorus_synthesis_info_new'
+input('TABLE_NAME = {} ?'.format(TABLE_NAME))
+
+cur_dir = os.path.dirname(os.path.abspath(__file__))
+
+# MySQL connection setup
+mysql_connection = mysql.connector.connect(
+    host='100.84.94.73',
+    user='metadata_mat_papers',
+    password='siat-mic',
+    database='metadata_mat_papers'
+)
+
+try:
+    mysql_cursor = mysql_connection.cursor()
+    
+    # 获取所有已转换的 doi
+    query = f"SELECT doi, md_url FROM {TABLE_NAME} WHERE en_text_content IS NOT NULL;"
+    mysql_cursor.execute(query)
+    results = mysql_cursor.fetchall()
+    dois = [row[0] for row in results]
+    md_urls = [row[1] for row in results]
+
+    for doi, md_url in tqdm.tqdm(zip(dois, md_urls), total=len(dois)):
+        # 若是已经修改过的，则直接跳过
+        dir_name = 'phosphorus'
+        if md_url is not None and md_url.split('/')[0] == dir_name and md_url.split('/')[1] == 'mds':
+            continue
+        md_name = doi.replace('/','_').replace('<','_').replace('>','_').replace(':','_')
+        md = md_name + '.md'
+        md_path = os.path.join(dir_name+'/mds', md_name, md)
+        query = f"UPDATE {TABLE_NAME} SET md_url = '{md_path}', convert2md = 'success' WHERE doi = '{doi}';"
+        mysql_cursor.execute(query)
+        mysql_connection.commit()
+
+    # 提交更改到数据库
+    mysql_connection.commit()
+
+except mysql.connector.Error as error:
+    print("Failed to insert record into MySQL table: {}".format(error))
+    # 如果发生错误，撤回事务
+    mysql_connection.rollback()
+
+finally:
+    # 关闭游标和连接
+    mysql_cursor.close()
+    mysql_connection.close()