I am trying to make a query for my PostgreSQL database.
I think the format of my query is wrong and I can't seem to get it to work, I have posted my code below:
query = cur.execute('SELECT "KINASE_NAME" FROM public."Phosphosite_table"
WHERE "GENE_NAME" LIKE %(genename)s AND "RESIDUE" LIKE %(location)s')
The aim is to take the kinase name is the gene name and location match.
my error message appears as the following:
ProgrammingError Traceback (most recent call last)
<ipython-input-33-9eae43b913d6> in <module>()
35 cur = connection.cursor()
36
---> 37 query = cur.execute('SELECT "KINASE_NAME" FROM public."Phosphosite_table" WHERE "GENE_NAME" LIKE%(genename)s AND "RESIDUE" LIKE %(location)s')
Thanks!
Connor
Don't use string operations to build SQL queries. Use the proper %s syntax.
genname = "foo"
location = "bar"
cur.execute("SELECT ... LIKE %s and ... LIKE %s", (genname, location))
No quotes around the values must be used. The quoting will be done by the DB API library.
Related
Not sure if this is a Supabase issue or a psycopg2 issue honestly and would love some help debugging.
I have the following code:
args = [('HaurGlass','60000','2022-10-20T21:15:39.751Z','10130506261','ac76e8db-ace0-40df-b6fa-f470641805e9','ad43639e-f66e-49d5-8fe8-d1ce5cd26193','{}')]
statement = ('''
INSERT INTO %s (%s) VALUES %s ON CONFLICT (company_id, crm_id)
DO UPDATE SET (%s)=(%s) RETURNING crm_id, id''')
statement = cur.mogrify(statement,
(AsIs(db_table), AsIs(','.join(keys)),
AsIs("%s"), AsIs(','.join(update_keys)),
AsIs(','.join(excluded_keys))))
output = execute_values(cur, statement, args, fetch=True)
The weird thing is that if args is <=100 rows in length, this query works without any problems. As soon as I increase the length of args to 101 rows or more, my Postgres logs show:
INSERT INTO licenses (name,value,subscription_end,crm_id,company_id,csm_id,custom_data) VALUES ('HaurGlass','60000','2022-10-20T21:15:39.751Z','10130506261','ac76e8db-ace0-40df-b6fa-f470641805e9','ad43639e-f66e-49d5-8fe8-d1ce5cd26193','{}')...
which would be good, except that it's immediately followed by:
INSERT INTO licenses (name,value,subscription_end,crm_id,company_id,csm_id,custom_data) VALUES ('HaurGlass','60000','2022-10-20T21:15:39.751Z','10130506261','ac76e8db-ace0-40df-b6fa-f470641805e9',NULL,'{}'),...
I've also confirmed that the number of records in the second "NULLifying" query is exactly equal to len(args)-100.
Any idea what is going on?
OK so it turns out I was missing the page_size parameter. All I had to do was:
output = execute_values(cur, statement, args, fetch=True, page_size=len(args))
I have a JPA/Springboot application backed by a Postgres database. I need to get a records that is equal to a substring passed back to the server.
For example:
Select * from dp1_attachments where TRIM(RIGHT(dp1_submit_date_dp1_number::text, 5)) ='00007'
This query works in PgAdmin, but not in the JPA #Query statement.
#Query("SELECT a.attachmentsFolder as attachmentsFolder, a.attachmentNumber as attachmentNumber, a.attachmentName as attachmentName, a.dp1SubmitDateDp1Number as dp1SubmitDateDp1Number,a.attachmentType as attachmentType, a.attachmentDate as attachmentDate, a.attachmentBy as attachmentBy "
+ "FROM DP1Attachments a WHERE TRIM(SUBSTRING(a.dp1SubmitDateDp1Number::text, 5 )) = :dp1Number")
I've also tried CASTing the parameter like this:
#Query("SELECT a.attachmentsFolder as attachmentsFolder, a.attachmentNumber as attachmentNumber, a.attachmentName as attachmentName, a.dp1SubmitDateDp1Number as dp1SubmitDateDp1Number,a.attachmentType as attachmentType, a.attachmentDate as attachmentDate, a.attachmentBy as attachmentBy "
+ "FROM DP1Attachments a WHERE TRIM(SUBSTRING(CAST(a.dp1SubmitDateDp1Number as string, 5 ))) = :dp1Number")
but the application won't even run, and returns an error that the query isn't valid.
If I make no attempt to cast it, I get an error that function pg_catalog.substring(numeric, integer) does not exist
UPDATE
I've also tried creating a native query instead but that also doesn't seem to work.
List<DP1AttachmentsProjection> results = em.createNativeQuery("Select * FROM dp1_attachments WHERE TRIM(RIGHT(CAST(dp1_submit_date_dp1_number as varchar),5)) =" + dp1Number).getResultList();
In place of varchar I have also tried string and text.
Errors come back similar to ERROR: operator does not exist: text = integer. Its like the CAST is being ignored and I'm not sure why.
I also tried the following as a native query:
em.createNativeQuery("Select * FROM dp1_attachments WHERE TRIM(RIGHT(dp1_submit_date_dp1_number::varchar),5)) =" + dp1Number).getResultList();
and get ERROR: syntax error at or near ":"
FINAL SOLUTION
Thanks to #Nenad J I altered the query to get the final working solution:
#Query(value = "SELECT a.attachments_Folder as attachmentsFolder, a.attachment_Number as attachmentNumber, a.attachment_Name as attachmentName, a.dp1_Submit_Date_Dp1_Number as dp1SubmitDateDp1Number,a.attachment_Type as attachmentType, a.attachment_Date as attachmentDate, a.attachment_By as attachmentBy FROM DP1_Attachments a WHERE TRIM(RIGHT(CAST(a.dp1_Submit_Date_Dp1_Number as varchar ), 5 )) = :dp1Number", nativeQuery = true)"
Default substring returns a string, so substring(integer data,5) returns a string. Thus no need for the cast.
#Query("SELECT * FROM DP1Attachments a WHERE TRIM(SUBSTRING(a.dp1SubmitDateDp1Number, 5)) = :dp1Number")
But I recommend in this case use native query like this:
Put this code in your attachment repository.
#Query(value="SELECT * FROM DP1Attachments AS a WHERE TRIM(SUBSTRING(a.dp1SubmitDateDp1Number, 5 )) = :dp1Number", nativeQuery=true)
Be careful with the column's name.
I am trying to pipe a webscraped pandas dataframe into a MySql table with mysql.connector but I can't seem to link df values to the %s variable. The connection is good (I can add individual rows) but it just returns errors when I replace the value witht he %s.
cnx = mysql.connector.connect(host = 'ip', user = 'user', passwd = 'pass', database = 'db')
cursor = cnx.cursor()
insert_df = ("""INSERT INTO table"
"(page_1, date_1, record_1, task_1)"
"VALUES ('%s','%s','%s','%s')""")
cursor.executemany(insert_df, df)
cnx.commit()
cnx.close()
This returns "ValueError: The truth value of a DataFrame is ambiguous. Use a.empty, a.bool(), a.item(), a.any() or a.all()."
If I add any additional oiperations it returns "ProgrammingError: Parameters for query must be an Iterable."
I am very new to this so any help is appreciated
Work around for me was to redo my whole process. I ran sqlalchemy, all the documentation makes this very easy. message if you want the code I used.
I'm getting SQL exception while executing the query which contains
split_part() method as split_part(value::TEXT,':', 1).
String queryStr = " select split_part(value::TEXT,':', 1) from table";
Query query = entityManager.createNativeQuery(queryStr);
List results = query.getResultList();
ERROR 2020-02-10 14:54:37,926 [http-nio-7070-exec-1] 142 - ERROR: syntax error at or near ":"
Position: 855
Your obfuscation layer probably chokes on the :: operator. Use the cast() operator instead:
String queryStr = " select split_part(cast(value as text),':', 1) from table";
But why do you think you need the cast to begin with? If you are storing : characters that column, it is most probably a text (or varchar) column anyway and you don't need a cast at all.
I'm using psycopg2 to query a database that starts with a number + ".district", so my code goes like:
number = 2345
cur = conn.cursor()
myquery = """ SELECT *
FROM {0}.districts
;""".format(number)
cur.execute("""{0};""".format(query))
data = cur.fetchall()
conn.close()
And i keep receiving the following psycopg2 error..
psycopg2.ProgrammingError: syntax error at or near "2345."
LINE 1: SELECT * FROM 2345.districts...
Thought it was the type of data the problem, maybe int(number) or str(number)..but no, same error appears.
¿ What am i doing wrong ?
The way you are trying to use to pass parameters is not supported. Please read the docs.