Initial Geo_Db Changes

geodb_pipeline/new_json_generator.py

@@ -0,0 +1,125 @@
+import sqlite3
+import json
+import csv
+from sqlite3 import Error
+
+def create_connection(db_file):
+    """ create a database connection to the SQLite database
+        specified by the db_file
+    :param db_file: database file
+    :return: Connection object or None
+    """
+    try:
+        conn = sqlite3.connect(db_file)
+        return conn
+    except Error as e:
+        print(e)
+
+    return None
+
+def select_ten_tasks(conn):
+    """
+    Query 10 rows in the tasks table
+    :param conn: the Connection object
+    :return:
+    """
+    cur = conn.cursor()
+    cur.execute("SELECT * FROM gsm limit 10")
+
+    rows = cur.fetchall()
+
+    for row in rows:
+        print(row)
+
+def select_json(conn,gpl_list):
+    """
+    Query rows in the gsm table to get the title, sample and charateristics 
+    :param conn: the Connection object
+    :return:
+    """
+    gpl_list_str = ",".join([str(x) for x in gpl_list])
+    print(gpl_list_str)
+    cur = conn.cursor()
+    #gpl_list = gpl_list[1:2]
+    gpl_size = 0
+    for item in gpl_list:
+        print (gpl_size)
+        cur.execute('select gsm,title,type,source_name_ch1,characteristics_ch1 from gsm where gpl=?',(item,))
+        rows = cur.fetchall()
+        count = 0
+        shrunk_json = []
+        dummy_json = []
+
+        for row in rows:
+            dummy_json = []
+            count2 = 1
+            for key in cur.description:
+                if(key[0] == 'gsm'): 
+                    #print (key)
+                    #print("here....")
+                    #print(key[0])
+                    continue
+                #print (type(key[0]))
+                #print(key)
+                dummy_json.append({key[0]:row[count2]})
+                count2=count2+1
+            shrunk_json.append({row[0]:dummy_json})
+        file_name = 'gpl_files/{}.json'.format(gpl_size)
+        with open(file_name, 'w') as outfile:
+            d = json.dumps({item:shrunk_json})
+            json.dump(json.loads(d), outfile)
+        gpl_size = gpl_size+1
+        # count = count+1
+        # if count==10 :
+        #         break
+    return 0
+
+def supported_microarray_csv2list(csv_file):
+    """
+    Get list of external_accession from the supported microarray platforms for human only
+    :param file: A csv file
+    :return: the list of rows in column 2
+    """
+    count = 0
+    ans = []
+    with open(csv_file) as csvfile:
+        readCSV = csv.reader(csvfile, delimiter=',')
+        for row in readCSV:
+                #print(row)
+                ans.append(row[1])
+
+    return ans[1:]
+
+def main():
+    """
+    This is the main function that returns a json object with limited columns for the current list of supported_microarray as of 25 May
+    :param 
+    :return: json object
+    """    
+    supported_microarray_csv_file = "supported_microarray.csv"
+    supported_microarray_list = supported_microarray_csv2list(supported_microarray_csv_file)
+    print(len(supported_microarray_list))
+    print(len(set(supported_microarray_list)))
+    #for item in supported_microarray_list:
+    #   print(item)
+    database = "GEOmetadb.2019-04-22.sqlite"
+
+    # create a database connection
+    conn = create_connection(database)
+    json_content = ""
+    with conn:
+        print("1. Query 10 tasks")
+        #select_ten_tasks(conn)
+        select_json(conn,supported_microarray_list)
+    # d = json.loads(json_content)
+    # print(len(d))
+    # print(len(d['shrunk_json']))
+    # print((d['shrunk_json'][0]))
+    # print(d['shrunk_json'][0]['GSM3463220'])
+    # with open('data1.json', 'w') as outfile:
+    #     json.dump(d, outfile)
+    # return d
+
+if __name__ == '__main__':
+    main()
+