Using psql with COPY FROM STDIN works fine when executed via -c (inline command) but the same thing fails if -f (script file) is used. I've created a Docker-based test to demonstrate below; tested on MacOS w/ zsh and Debian w/ bash.
I was unable to find any relevant documentation on why this would be but I imagine it has to do with psql's special \copy functionality. Can someone help illuminate me?
# create test data
echo "1,apple
2,orange
3,banana">testdata.csv
# create test script
echo "drop table if exists fruits;
create table fruits (id INTEGER, name VARCHAR);
copy fruits from stdin with delimiter as ',' csv;
select * from fruits">testscript.pg
# create network
docker network create pgtest
# run Postgres server
echo "starting postgres server"
PG_CONTAINER_ID=$(docker run -d --name=pgtest --rm --network=pgtest -h database -e POSTGRES_USER=user1 -e POSTGRES_PASSWORD=pass1 -e POSTGRES_DB=db1 -p 6432:5432 postgres:12)
echo "sleeping for 5 seconds (wait for server to start)"
sleep 5
docker logs $PG_CONTAINER_ID
echo "*"
echo "*"
echo "*"
echo "run psql script using inline with -c"
cat testdata.csv | docker run -i --rm --network=pgtest postgres:12 psql postgres://user1:pass1#database:5432/db1 -c "$(cat testscript.pg)"
echo "*"
echo "*"
echo "*"
echo "run psql script using file with -f"
cat testdata.csv | docker run -i -v $PWD:/host --rm --network=pgtest postgres:12 psql postgres://user1:pass1#database:5432/db1 -f /host/testscript.pg
# stop server
echo "*"
echo "*"
echo "*"
docker stop $PG_CONTAINER_ID
docker rm $PG_CONTAINER_ID
The output of the psql commands look like this:
*
*
*
run psql script using inline with -c
NOTICE: table "fruits" does not exist, skipping
id | name
----+--------
1 | apple
2 | orange
3 | banana
(3 rows)
*
*
*
run psql script using file with -f
DROP TABLE
CREATE TABLE
psql:/host/testscript.pg:5: ERROR: invalid input syntax for type integer: "select * from fruits"
CONTEXT: COPY fruits, line 1, column id: "select * from fruits"
In the first case, (execution with -c), the copy data are read from standard input.
In the second case (execution with -f), the input file acts as input to psql (if you want, standard input is redirected from that file). So PostgreSQL interprets the rest of the file as COPY data and complains about the content. You'd have to mix the COPY data in with the file:
/* script with copy data */
COPY mytable FROM STDIN (FORMAT 'csv');
1,item 1,2021-11-01
2,"item 2, better",2021-11-11
\.
/* next statement */
ALTER TABLE mytable ADD newcol text;
Related
I'd love to run pgadmin4 in our infrastructure in a way, that postgres servers would be preconfigured during docker build/1.st start.
I've tried to modify the internaly used /var/lib/pgadmin/pgadmin4.db sqlite DB on the 1.st start, which however results in an error in the UI (once selecting the particular postgres server:
definition of service "" not found
I've tried following:
Directory structure:
find ./ -print | sed -e 's;[^/]*/;|____;g;s;____|; |;g'
|____
|____dump
| |____servergroup.csv
| |____server.csv
| |____import_db.sh
|____Dockerfile
Where Dockerfile is:
cat Dockerfile
# rebuild:
# docker build -t pgadmin4:3.0-custom .
# run:
# docker run --rm -it -e PGADMIN_DEFAULT_EMAIL=admin -e PGADMIN_DEFAULT_PASSWORD=admin -p8081:80 docker build -t pgadmin4:3.0-custom
FROM dpage/pgadmin4:3.0
COPY dump/ /dump
RUN \
apk add --no-cache sqlite && \
chmod +x /dump/import_db.sh && \
# re rely on the current entrypoint.sh impl
sed -i '/python run_pgadmin.py/a \/dump\/import_db.sh' /entrypoint.sh && \
cat /entrypoint.sh
In fact it just modifies the https://github.com/postgres/pgadmin4/blob/master/pkg/docker/entrypoint.sh to run import_db.sh script on the 1.st start.
Where dump/import_db.sh is:
cat dump/import_db.sh
#!/bin/sh
echo ".tables" | sqlite3 -csv /var/lib/pgadmin/pgadmin4.db
# remove header and `1,1,Servers` entry (would cause duplicates)
cat /dump/servergroup.csv | sed '1d' | grep -v 1,1,Servers > /tmp/servergroup.in.csv
echo "csv servergroup:"
cat /tmp/servergroup.in.csv
echo "DB servergroup:"
sqlite3 -csv -header /var/lib/pgadmin/pgadmin4.db "select * from servergroup;"
echo ".import /tmp/servergroup.in.csv servergroup" | sqlite3 -csv /var/lib/pgadmin/pgadmin4.db
# remove header
cat /dump/server.csv | sed '1d' > /dump/server.in.csv
echo "csv server:"
cat /dump/server.in.csv
echo "DB server:"
sqlite3 -csv -header /var/lib/pgadmin/pgadmin4.db "select * from server;"
echo ".import /dump/server.in.csv server" | sqlite3 -csv /var/lib/pgadmin/pgadmin4.db
Csv files contents:
cat dump/server.csv
id,user_id,servergroup_id,name,host,port,maintenance_db,username,password,role,ssl_mode,comment,discovery_id,hostaddr,db_res,passfile,sslcert,sslkey,sslrootcert,sslcrl,sslcompression,bgcolor,fgcolor,service
1,1,2,servername,localhost,5432,postgres,postgres,"",,prefer,,,"","",,<STORAGE_DIR>/.postgresql/postgresql.crt,<STORAGE_DIR>/.postgresql/postgresql.key,,,0,,,
cat dump/servergroup.csv
id,user_id,name
2,1,my-group
1,1,Servers
Any idea how to fix my error? Or of any other approach that could provide me the pre-configured pgadmin4 docker container?
The current version of image dpage/pgadmin is 4.24. This version has support for external configuration of server definition list (servers.json):
{
"Servers": {
"test": {
"Name": "test",
"Group": "Servers",
"Port": 5432,
"Username": "postgres",
"Host": "postgres",
"SSLMode": "prefer",
"MaintenanceDB": "postgres"
}
}
}
Volume binding can be configured as below:
volumes:
- ./servers.json:/pgadmin4/servers.json
First time container is started server groups and servers will be configured automaticaly.
UPD. JSON format has more fields which are optional. It's important that password can not be imported/exported in such way due to the obvious security reasons.
Looks this change the service column value to an empty string instead of NULL.
Can you try updating the value of service column to NULL
sqlite> UPDATE server SET service = NULL;
commit the changes and Restart pgAdmin4 & try again connecting to that server.
I have created a bash script to copy CSV data into a Postgres table.
#!/bin/sh
PSQL=/Library/PostgreSQL/13/bin/psql
DB_USER=user
DB_HOST=localhost
DB_NAME=dbname
export PGPASSWORD="password"
file_path="/Users/user/test.csv"
echo "copy started .."
result=$($PSQL -X -U $DB_USER -h $DB_HOST -P t -P format=unaligned -c "\\COPY table_name FROM '$file_path' DELIMITER ',' CSV HEADER" $DB_NAME)
echo "copy completed : $result"
This always returns COPY 0 and no records are added.
Tried running the copy command on terminal as well but same result.
I am missing something here?
Suppose I created a sequence in postgresql:
CREATE SEQUENCE my_seq;
I store the below line in an sql file get_seq.sql
SELECT last_value FROM my_seq;
$SUDO psql -q -d database_bame -f get_seq.sql
How do I get the int number returned by SELECT into bash and use it?
You can capture the result of a command using the VAR=$(command) syntax:
VALUE=$(psql -qtAX -d database_name -f get_seq.sql)
echo $VALUE
The required psql options mean:
-t only tuple
-A output not unaligned
-q quiet
-X Don't run .psqlrc file
Try:
LAST_VALUE=`echo "SELECT last_value FROM my_seq;" | psql -qAt -d database_name`
I want to store following postgreSQL query result in a variable. I am writing command on the shell script.
psql -p $port -c "select pg_relation_size ('tableName')" postgres
I need variable to save the result on a file. I have tried following but it is not working
var= 'psql -p $port -c "select pg_relation_size ('tableName')" '
Use a shell HERE document like:
#!/bin/sh
COUNT=`psql -A -t -q -U username mydb << THE_END
SELECT count (DISTINCT topic_id) AS the_count
FROM react
THE_END`
echo COUNT=${COUNT}
The whole psql <<the_end ... stuff here ... the_end statement is packed into backticks
the output of the execution of the statement inside the backticks is used as a value for the COUNT shell variable
The -A -t -q are needed to suppress column headers and error output
inside a here document, shell variable substitution works, even in single quotes!
So, you could even do:
#!/bin/sh
DB_NAME="my_db"
USR_NAME="my_name"
TBL_NAME="my_table"
COL_NAME="my_column"
COUNT=`psql -A -t -q -U ${USR_NAME} ${DB_NAME} << THE_END
SELECT COUNT(DISTINCT ${COL_NAME} ) AS the_count
FROM ${TBL_NAME}
THE_END`
echo COUNT=${COUNT}
to run a query inline you have to wrap it in grave accents, not single quotes:
$ vim `which fancyexecfileinpath`
psql lets you run queries from command line, but I guess you should be inputting complete information. you might be missing the database name.
postgres#slovenia:~$ psql -d mydbname -c "select * from applications_application;"
postgres#slovenia:~$ specialvar=`psql -d flango -c "select * from applications_application;"`
postgres#slovenia:~$ echo $specialvar
id | name | entities | folder | def_lang_id | ... | 2013-07-09 15:16:57.33656+02 | /img/app3.png (1 row)
postgres#slovenia:~$
notice the grave accents when assigning it to specialvar
otherwise you'll be setting it to a string.
There shouldn't be any space between the variable and the equals sign ("=") and the value ( http://genepath.med.harvard.edu/mw/Bash:HOW_TO:_Set_an_environment_variable_in_the_bash_shell )
For instance, I have a table stores value:
select * from myvalue;
val
-------
12345
(1 row)
How can I save this 12345 into a variable in postgresql or shell script?
Here's what I tried in my shell script:
var=$(psql -h host -U user -d db <<SQLSTMT
SELECT * FROM myvalue;
SQLSTMT)
but echo $var gives me:
val ------- 12345 (1 row)
I've also tried
\set var (select * from myvalue)
in psql and when I type \set it lists:
var = '(select*frommyvalue)'
No, no, no! Use "raw data" switch from psql, like "-t" or "\t" and pipe the query to psql instead of parsing ascii-table, come on :-)
echo 'select * from myvalue;' | psql -t -h host -U user -d db
If you really need parse psql output, you could also use -H switch ( turns on HTML output ), and parse it with some perl module for parsing html tables, I used that once or twice.. Also, you may want to use a pgpass file and ~/.psqlrc for some defaults, like default DB to connect, when not specified.
psql has a -c/--command= option to accept SQL from the command line, and -t/--tuples-only option to control output formatting.
$ psql -c 'select 1+1'
?column?
----------
2
(1 row)
$ psql -t -c 'select 1+1'
2
$ VALUE=`psql -t -c 'select 1+1'`
$ echo $VALUE
2
var=`psql -Atc "select 1;"`
echo $var
1
In this answer I explain one way to do it, using a co-process to communicate back-and-forth with psql. That's overkill if all you need is to run a query and get a single result, but might be good to know if you're shell scripting with psql.
You can filter the result you get with your psql command:
var=$(psql -h host -U user -d db <<SQLSTMT
SELECT * FROM myvalue;
SQLSTMT)
var=$(cut -d' ' -f3 <<<$var)
None of these worked for me, but this did:
median_avm=psql "host=${dps1000} port=#### dbname=### user=${reduser} password=${redpass}" -c "SELECT AVG(column) FROM db.table;" -t
using a source file with ${dps1000}, ${reduser}, ${redpass} defined and manually entering port and dbname