Archive for the ‘Python’ Category
Installing PL/Python Extension
While PL/Python is an untrusted language inside PostgreSQL, I was installing it to test some of its features. First, we check to see if PL/Python is installed by attempting to create a PL/Python function:
CREATE FUNCTION pima(a integer, b integer) RETURNS integer AS $$ if a > b: return a return b $$ LANGUAGE plpython3u; |
It likely should raise an error like this because PL/Python is an untrusted language. It’s untrusted because it runs with root
privileges rather than a restricted user’s privilege. More or less, with PL/Python you can access the entire database. This makes PL/Python more of a threat than tool beyond experimentation in a test database.
ERROR: language "plpython3u" does not exist HINT: Use CREATE EXTENSION to load the language into the database. |
A quick query as the postgres user tells you whether or not PL/Python is installed:
SELECT * FROM pg_language; |
It returns the following:
lanname | lanowner | lanispl | lanpltrusted | lanplcallfoid | laninline | lanvalidator | lanacl ----------+----------+---------+--------------+---------------+-----------+--------------+-------- internal | 10 | f | f | 0 | 0 | 2246 | c | 10 | f | f | 0 | 0 | 2247 | sql | 10 | f | t | 0 | 0 | 2248 | plpgsql | 10 | t | t | 14088 | 14089 | 14090 | (4 rows) |
I attempted to add PL/Python with the following command:
CREATE EXTENSION plpython3u; |
It raised the following error:
ERROR: could not open extension control file "/usr/pgsql-11/share/extension/plpython3u.control": No such file or directory |
The error basically appeared to occur because there’s a missing Python 3 package from what I could find on the web. I installed the missing postgresql-plpython3
package as the root
superuser, which you also could install as a member of the sudoer list. The following shows how to install it as a sudoer member:
sudo yum install -y postgresql-plpython3 |
You should see something close to the following console output:
Last metadata expiration check: 0:43:53 ago on Fri 06 Nov 2020 10:42:28 AM MST. Dependencies resolved. ============================================================================================================ Package Architecture Version Repository Size ============================================================================================================ Installing: postgresql-plpython3 x86_64 11.7-2.fc30 updates 86 k Installing dependencies: postgresql-server x86_64 11.7-2.fc30 updates 5.3 M Transaction Summary ============================================================================================================ Install 2 Packages Total download size: 5.3 M Installed size: 23 M Downloading Packages: (1/2): postgresql-plpython3-11.7-2.fc30.x86_64.rpm 218 kB/s | 86 kB 00:00 (2/2): postgresql-server-11.7-2.fc30.x86_64.rpm 3.0 MB/s | 5.3 MB 00:01 ------------------------------------------------------------------------------------------------------------ Total 2.1 MB/s | 5.3 MB 00:02 Running transaction check Transaction check succeeded. Running transaction test Transaction test succeeded. Running transaction Preparing : 1/1 Running scriptlet: postgresql-server-11.7-2.fc30.x86_64 1/2 Installing : postgresql-server-11.7-2.fc30.x86_64 1/2 warning: /var/lib/pgsql/.bash_profile created as /var/lib/pgsql/.bash_profile.rpmnew Running scriptlet: postgresql-server-11.7-2.fc30.x86_64 1/2 Installing : postgresql-plpython3-11.7-2.fc30.x86_64 2/2 Running scriptlet: postgresql-plpython3-11.7-2.fc30.x86_64 2/2 Verifying : postgresql-plpython3-11.7-2.fc30.x86_64 1/2 Verifying : postgresql-server-11.7-2.fc30.x86_64 2/2 Installed: postgresql-plpython3-11.7-2.fc30.x86_64 postgresql-server-11.7-2.fc30.x86_64 Complete! |
While I thought this might fix the problem, it didn’t and raised the following error:
ERROR: could not open extension control file "/usr/pgsql-11/share/extension/plpython3u.control": No such file or directory |
I found the plpython3u.control
file on GitHub and put the following plpython3u.control
file, after comparing it against the plpgsql.control
file, into the /usr/pgsql-11/share/extension
directory. At this point, I began wondering why it’s looking in the /usr/pgsql-11/share/extension
directory instead of a /usr/plpython3u/share/extension
directory (does not exist).
# plpython3u extension comment = 'PL/Python3U untrusted procedural language' default_version = '1.0' module_pathname = '$libdir/plpython3' relocatable = false schema = pg_catalog superuser = true |
I retried creating the plpython3u
extension:
CREATE EXTENSION plpython3u; |
It raised the following error:
ERROR: extension "plpython3u" has no installation script nor update path for version "1.0" |
At this point, I could find no further help on the Internet. I did notice that there were these two *.sql
files in the /usr/pgsql-11/share/extension
directory:
- plpgsql–1.0.sql
- plpgsql–unpackaged–1.0.sql
I found this plpython3u--1.0.sql
file on GitHub:
/* src/pl/plpython/plpython3u--1.0.sql */ CREATE FUNCTION plpython3_call_handler() RETURNS language_handler LANGUAGE c AS 'MODULE_PATHNAME'; CREATE FUNCTION plpython3_inline_handler(internal) RETURNS void STRICT LANGUAGE c AS 'MODULE_PATHNAME'; CREATE FUNCTION plpython3_validator(oid) RETURNS void STRICT LANGUAGE c AS 'MODULE_PATHNAME'; CREATE LANGUAGE plpython3u HANDLER plpython3_call_handler INLINE plpython3_inline_handler VALIDATOR plpython3_validator; COMMENT ON LANGUAGE plpython3u IS 'PL/Python3U untrusted procedural language'; |
I retried creating the plpython3u
extension, as a member of the sudoer list and got a new error:
ERROR: permission denied to create extension "plpython3u" HINT: Must be superuser to create this extension. |
I retried creating the plpython3u
extension as the postgres
user, who is the owning user:
CREATE EXTENSION plpython3u; |
It raised the following error:
ERROR: could not access file "$libdir/plpython3": No such file or directory |
While I intend to finish this, that’s as far as I got. It appears from some of the things I’ve read I need to recompile or configure items that would destabilize what I have working at the moment. Finishing this will need to wait for me to build another test environment from scratch. If you catch this post and know the remaining steps, I invite you to add them in the comments.
Quick Python Flask
A quick example of installing and running a sample hello.py
file with the Flask application with the Command Line Interface (CLI) documentation on the Flask website. The first thing you need to do is install the flask module with the pip3
utility on Fedora Linux (or most other platforms):
pip3 install flask --user student |
You should see a successful log like this for student
user:
Requirement already satisfied: flask in /usr/local/lib64/python3.7/site-packages (1.1.2) Collecting student Downloading https://files.pythonhosted.org/packages/b5/af/be416c18e4fe63a582e06fb0d47bf059bd0f4f413e5a6cfe893747ebaf79/Student-0.0.1-py3-none-any.whl Requirement already satisfied: click>=5.1 in /usr/lib/python3.7/site-packages (from flask) (7.1.1) Requirement already satisfied: itsdangerous>=0.24 in /usr/local/lib/python3.7/site-packages (from flask) (1.1.0) Requirement already satisfied: Werkzeug>=0.15 in /usr/local/lib/python3.7/site-packages (from flask) (1.0.1) Requirement already satisfied: Jinja2>=2.10.1 in /usr/lib/python3.7/site-packages (from flask) (2.10.1) Requirement already satisfied: MarkupSafe>=0.23 in /usr/lib64/python3.7/site-packages (from Jinja2>=2.10.1->flask) (1.1.1) Installing collected packages: student Successfully installed student-0.0.1 |
The smallest footprint hello.py
program is:
# Import statement. from flask import Flask # Application defintion. app = Flask(__name__) # Basic URI rotuing. @app.route("/") # Define a hello function. def hello(): return "Hello World!" # Run the program. if __name__ == "__main__": app.run() |
You can run the program from the command line with two commands:
export FLASK_APP=hello.py flask run |
It will show you the following in the terminal session:
* Serving Flask app "hello.py" * Environment: production WARNING: This is a development server. Do not use it in a production deployment. Use a production WSGI server instead. * Debug mode: off * Running on http://127.0.0.1:5000/ (Press CTRL+C to quit) |
Type the following URL in a local browser:
http://localhost:5000/ |
Flask will add the following to the console log:
127.0.0.1 - - [26/Oct/2020 00:37:49] "GET / HTTP/1.1" 200 - |
You can jazz the hello.py
program up with a an argument list, like this modified example based on this comparison article on Python frameworks:
# Import libraries. from flask import Flask, escape, request # Define the application. app = Flask(__name__) # Define a base URI route and function. @app.route('/') def index(): return "Index Page" # Define an application URI route and function. @app.route("/hello") def hello(): name = request.args.get("name","Simon") return f'Hello {escape(name)}!' # Define an about URI route and function. @app.route("/about") def about(): return "About Page" # Run the file. if __name__ == "__main__": app.run() |
It prints 'Hello Simon!'
in a web page. If you try to stop your Flask server with a Ctrl+Z
instead of a Ctrl+C
, the next time you go to start it you will receive an error message like:
OSError: [Errno 98] Address already in use |
You’ll need to find the Linux process ID and kill the process with prejudice. You can find the process with the following Linux command:
sudo netstat -nlp | grep 5000 [sudo] password for student: |
It prompts you for your sudoer password, and then returns a line like:
tcp 0 0 127.0.0.1:5000 0.0.0.0:* LISTEN 76802/python3 |
You kill the process with the following Linux command:
kill -9 76802 |
As always, I hope this helps those looking for the missing pieces.
Wrap Oracle’s tnsping
If you’ve worked with the Oracle database a while, you probably noticed that some utilities write to stdout
for both standard output and what should be standard error (stderr
). One of those commands is the tnsping
utility.
You can wrap the tnsping
command to send the TNS-03505
error to stdout
with the following code. I put Bash functions like these in a library.sh
script, which I can source when automating tasks.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 | #!/usr/bin/bash tnsping() { if [ ! -z ${1} ]; then # Set default return value. stdout=`$ORACLE_HOME/bin/tnsping ${1} | tail -1` # Check stdout to return 0 for success and 1 for failure. if [[ `echo ${stdout} | cut -c1-9` = 'TNS-03505' ]]; then python -c 'import os, sys; arg = sys.argv[1]; os.write(2,arg + "\n")' "${stdout}" else echo "${1}" fi fi } |
You should notice that the script uses a Python call to redirect the error message to standard out (stdout
) but you can redirect in Bash shell with the following:
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 | #!/usr/bin/bash tnsping() { if [ ! -z ${1} ]; then # Set default return value. stdout=`$ORACLE_HOME/bin/tnsping ${1} | tail -1` # Check stdout to return 0 for success and 1 for failure. if [[ `echo ${stdout} | cut -c1-9` = 'TNS-03505' ]]; then echo ${stdout} 1>&2 else echo "${1}" fi fi } |
Interactively, we can now test a non-existent service name like wrong
with this syntax:
tnsping wrong |
It’ll print the standard error to console, like:
TNS-03505: Failed to resolve name |
or, you can suppress standard error (stderr
) by redirecting it to the traditional black hole, like:
tnsping wrong 2>/dev/null |
After redirecting standard error (stderr
), you simply receive nothing back. That lets you evaluate in another script whether or not the utility raises an error.
In an automating Bash shell script, you use the source command to put the Bash function in scope, like this:
source library.sh |
As always, I hope this helps those looking for a solution.
Python List & Dictionaries
The following two sample programs are used in an Python programming course that I teach. I find them useful in qualifying how to work with loops, couple loops, and queues. The first example uses two lists and coupled loops, while the second example uses a single dictionary and FILO queue approach.
The Twelve Days of Christmas lyrics can be printed like so with coupled loops:
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 | days = ['first','second','third','fourth' \ ,'fifth','sixth','seventh','eighth' \ ,'nineth','tenth','eleventh','twelveth'] verse = ['partridge in a pear tree.' \ ,'Two turtle doves,' \ ,'Three French hens,' \ ,'Four calling birds,' \ ,'Five gold rings,' \ ,'Six geese a-laying,' \ ,'Seven swans a-swimming,' \ ,'Eight maids a-milking,' \ ,'Nine ladies dancing,' \ ,'Tenth lords a-leaping,' \ ,'Eleven pipers piping,' \ ,'Twelve drummers drumming,'] # Loop forward, couple inner loop, and loop backward through list. for i in range(0,len(days), 1): print("On the",str(days[i]),"day of Christmas my true love sent to me") for j in range(i, -1, -1): if (j > 0): print(" ",verse[j]) elif (i == j): print(" A",verse[j]) else: print(" and a",verse[j]) |
Recreating the problem into a single dictionary, you can solve by approaching it as a FILO queue. Here’s the approach:
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 | lyric = {'first':'partridge in a pear tree.' ,'second':'Two turtle doves,' ,'third':'Three French hens,' ,'fourth':'Four calling birds,' ,'fifth':'Five gold rings,' ,'sixth':'Six geese a-laying,' ,'seventh':'Seven swans a-swimming,' ,'eighth':'maids a-milking,' ,'nineth':'Nine ladies dancing,' ,'tenth':'Ten lords a-leaping,' ,'eleventh':'Eleven pipers piping,' ,'twelfth':'Twelve drummers drumming,'} # Intiate a list for collecting stanza. stanza = list() # Generate a list of keys. for i in lyric.keys(): # Append keys to list of stanza. stanza.append(i) # Print the first line of each stanza. print("On the",i,"day of Christmas my true love sent to me") # Print the progressive stanza. for j in reversed(stanza): if (j not in ['first','twelveth']): print(" ",lyric[j]) elif (i == j): print(" A",lyric[j]) else: print(" and a",lyric[j]) |
As always, I hope this helps for approaches and solutions.
Developing Python Libraries
I put this together to show my students how to simplify writing and testing Python library files. The trick requires that you learn how to set a relative $PYTHONPATH
environment file.
export set PYTHONPATH=./lib |
After setting the $PYTHONPATH
environment variable, connect to Python’s IDLE environment and run the following code:
import os print(os.environ['PYTHONPATH']) |
It prints the following:
./lib |
You can also discover all the standard libraries and your $PYTHONPATH
value in your environment with the following command:
for i in sys.path: print(i) |
It prints the following, which lists the one set by the $PYTHONPATH
first:
/home/student/Code/python/path/lib /usr/lib64/python37.zip /usr/lib64/python3.7 /usr/lib64/python3.7/lib-dynload /home/student/.local/lib/python3.7/site-packages /usr/lib64/python3.7/site-packages /usr/lib/python3.7/site-packages |
You create a test my_module.py
library file in the relative ./lib
directory, like the following:
# Define a hello function that accept a name and prints a salutation. def hello(whom): return "Hello " + whom + "!" |
Next, you can create a testlib.py
program:
# Import the hello function into the local namesapce from the my_module. from my_module import hello # Call the module hello, which returns a formatted string. print(hello("Suzie Q")) |
It imports the hello(whom)
function into the local namespace and then calls the hello(whom)
function with the string literal "Susie"
. It prints:
Hello Suzie Q! |
If you import
the my_module
module, you must refer to the hello(whom)
function by prefacing it with my_module.
, like the following example:
# Import the hello function into the local namesapce from the my_module. import my_module # Call the module hello, which returns a formatted string. print(my_module.hello("Suzie Q")) |
A direct import doesn’t add the method to the local namespace. It remains in the my_module
‘s namespace.
It’s probably important to note where my_module.pyc files are written for the those migrating from Python 2.7 to Python 3. In Python 2.7 they would be written to the ./lib
directory, but in Python 3 they’re written to the ./lib/__pycache__
directory.
As always, I hope this helps those who find it and read it.
Python-Postgres Query
As I committed to a student, here are sample programs for writing a Python query against the Postgres 11 database. The first one returns rows or tuples. The latter formats the text returned as columns.
If you’re one of many looking for the key psycopg2
driver library, you can find it in most distro repositories as: python3-psycopg2
. You can use dnf
or yum
to install it separately or you can install pgadmin4
, which includes the psycopg2
library.
The first example returns the entire row from a new_hire
table with two rows:
import psycopg2 try: # Open a connection to the database. connection = psycopg2.connect( user="student" , password="student" , port="5432" , dbname="videodb") # Open a cursor. cursor = connection.cursor() # Assign a static query. query = "SELECT * FROM new_hire" # Parse and execute the query. cursor.execute(query) # Fetch all rows from a table. records = cursor.fetchall() # Read through and print the rows as tuples. for row in range(0, len(records)): print(records[row]) except (Exception, psycopg2.Error) as error : print("Error while fetching data from PostgreSQL", error) finally: # Close the database connection. if (connection): cursor.close() connection.close() |
The first example returns the rows as tuples, which is probably desired if you want to consume the result in another Python program. Here’s the output retrieved:
(1001, 'Malcolm', 'Jacob', 'Lewis', datetime.date(2018, 2, 14)) (1002, 'Henry', None, 'Chabot', datetime.date(1990, 7, 31)) |
The second one returns the rows and formats the columns into output for a csv
style file:
import psycopg2 try: # Open a connection to the database. connection = psycopg2.connect( user="student" , password="student" , port="5432" , dbname="videodb") # Open a cursor. cursor = connection.cursor() # Assign a static query. query = "SELECT * FROM new_hire" # Parse and execute the query. cursor.execute(query) # Read through and print the formatted columns of each row. for (new_hire_id, first_name, middle_name, last_name, hire_date) in cursor: if (isinstance(middle_name,type(None))): print("{},'{} {}','{:%d-%b-%Y}'".format(new_hire_id, first_name, last_name, hire_date)) else: print("{},'{} {} {}','{:%d-%b-%Y}'".format(new_hire_id, first_name, middle_name, last_name, hire_date)) except (Exception, psycopg2.Error) as error : print("Error while fetching data from PostgreSQL", error) finally: # Close the database connection. if (connection): cursor.close() connection.close() |
The second one returns the rows and formatted columns for a csv
style file:
1001,'Malcolm Jacob Lewis','14-Feb-2018' 1002,'Henry Chabot','31-Jul-1990' |
As always, I hope these help those looking for a starting place with Python and Postgres.
pgAdmin4 on Fedora 30
While attempting an install of pgAdmin and updating a Fedora 30 environment, I encountered a conflict on the upgrade of MySQL 8.0.17-1 to 8.0.17.2. The community-mysql-8.0.17-2.fc30.x86_64
had conflicts with:
mysql-community-client-8.0.17-1.fc30.x86_64
packagemysql-community-server-8.0.17-1.fc30.x86_64
package
I tried to update the system before install pgadmin4
with the following syntax:
dnf -y update && dnf -y install pgadmin4 |
The dnf
utility raise the following MySQL package errors during transaction checking:
Display detailed console log →
Error: Transaction check error: file /usr/bin/mysql conflicts between attempted installs of community-mysql-8.0.17-2.fc30.x86_64 and mysql-community-client-8.0.17-1.fc30.x86_64 file /usr/bin/mysql_config_editor conflicts between attempted installs of community-mysql-8.0.17-2.fc30.x86_64 and mysql-community-client-8.0.17-1.fc30.x86_64 file /usr/bin/mysqladmin conflicts between attempted installs of community-mysql-8.0.17-2.fc30.x86_64 and mysql-community-client-8.0.17-1.fc30.x86_64 file /usr/bin/mysqlbinlog conflicts between attempted installs of community-mysql-8.0.17-2.fc30.x86_64 and mysql-community-client-8.0.17-1.fc30.x86_64 file /usr/bin/mysqlcheck conflicts between attempted installs of community-mysql-8.0.17-2.fc30.x86_64 and mysql-community-client-8.0.17-1.fc30.x86_64 file /usr/bin/mysqldump conflicts between attempted installs of community-mysql-8.0.17-2.fc30.x86_64 and mysql-community-client-8.0.17-1.fc30.x86_64 file /usr/bin/mysqlimport conflicts between attempted installs of community-mysql-8.0.17-2.fc30.x86_64 and mysql-community-client-8.0.17-1.fc30.x86_64 file /usr/bin/mysqlpump conflicts between attempted installs of community-mysql-8.0.17-2.fc30.x86_64 and mysql-community-client-8.0.17-1.fc30.x86_64 file /usr/bin/mysqlshow conflicts between attempted installs of community-mysql-8.0.17-2.fc30.x86_64 and mysql-community-client-8.0.17-1.fc30.x86_64 file /usr/bin/mysqlslap conflicts between attempted installs of community-mysql-8.0.17-2.fc30.x86_64 and mysql-community-client-8.0.17-1.fc30.x86_64 file /usr/bin/ibd2sdi conflicts between attempted installs of community-mysql-server-8.0.17-2.fc30.x86_64 and mysql-community-server-8.0.17-1.fc30.x86_64 file /usr/bin/innochecksum conflicts between attempted installs of community-mysql-server-8.0.17-2.fc30.x86_64 and mysql-community-server-8.0.17-1.fc30.x86_64 file /usr/bin/my_print_defaults conflicts between attempted installs of community-mysql-server-8.0.17-2.fc30.x86_64 and mysql-community-server-8.0.17-1.fc30.x86_64 file /usr/bin/myisam_ftdump conflicts between attempted installs of community-mysql-server-8.0.17-2.fc30.x86_64 and mysql-community-server-8.0.17-1.fc30.x86_64 file /usr/bin/myisamchk conflicts between attempted installs of community-mysql-server-8.0.17-2.fc30.x86_64 and mysql-community-server-8.0.17-1.fc30.x86_64 file /usr/bin/myisamlog conflicts between attempted installs of community-mysql-server-8.0.17-2.fc30.x86_64 and mysql-community-server-8.0.17-1.fc30.x86_64 file /usr/bin/myisampack conflicts between attempted installs of community-mysql-server-8.0.17-2.fc30.x86_64 and mysql-community-server-8.0.17-1.fc30.x86_64 file /usr/bin/mysql_secure_installation conflicts between attempted installs of community-mysql-server-8.0.17-2.fc30.x86_64 and mysql-community-server-8.0.17-1.fc30.x86_64 file /usr/bin/mysql_ssl_rsa_setup conflicts between attempted installs of community-mysql-server-8.0.17-2.fc30.x86_64 and mysql-community-server-8.0.17-1.fc30.x86_64 file /usr/bin/mysql_tzinfo_to_sql conflicts between attempted installs of community-mysql-server-8.0.17-2.fc30.x86_64 and mysql-community-server-8.0.17-1.fc30.x86_64 file /usr/bin/mysql_upgrade conflicts between attempted installs of community-mysql-server-8.0.17-2.fc30.x86_64 and mysql-community-server-8.0.17-1.fc30.x86_64 file /usr/bin/mysqld_pre_systemd conflicts between attempted installs of community-mysql-server-8.0.17-2.fc30.x86_64 and mysql-community-server-8.0.17-1.fc30.x86_64 file /usr/bin/perror conflicts between attempted installs of community-mysql-server-8.0.17-2.fc30.x86_64 and mysql-community-server-8.0.17-1.fc30.x86_64 file /usr/lib/systemd/system/mysqld.service conflicts between attempted installs of community-mysql-server-8.0.17-2.fc30.x86_64 and mysql-community-server-8.0.17-1.fc30.x86_64 file /usr/lib/systemd/system/mysqld@.service conflicts between attempted installs of community-mysql-server-8.0.17-2.fc30.x86_64 and mysql-community-server-8.0.17-1.fc30.x86_64 file /usr/lib64/mysql/plugin/adt_null.so conflicts between attempted installs of community-mysql-server-8.0.17-2.fc30.x86_64 and mysql-community-server-8.0.17-1.fc30.x86_64 file /usr/lib64/mysql/plugin/auth_socket.so conflicts between attempted installs of community-mysql-server-8.0.17-2.fc30.x86_64 and mysql-community-server-8.0.17-1.fc30.x86_64 file /usr/lib64/mysql/plugin/component_audit_api_message_emit.so conflicts between attempted installs of community-mysql-server-8.0.17-2.fc30.x86_64 and mysql-community-server-8.0.17-1.fc30.x86_64 file /usr/lib64/mysql/plugin/component_log_filter_dragnet.so conflicts between attempted installs of community-mysql-server-8.0.17-2.fc30.x86_64 and mysql-community-server-8.0.17-1.fc30.x86_64 file /usr/lib64/mysql/plugin/component_log_sink_json.so conflicts between attempted installs of community-mysql-server-8.0.17-2.fc30.x86_64 and mysql-community-server-8.0.17-1.fc30.x86_64 file /usr/lib64/mysql/plugin/component_log_sink_syseventlog.so conflicts between attempted installs of community-mysql-server-8.0.17-2.fc30.x86_64 and mysql-community-server-8.0.17-1.fc30.x86_64 file /usr/lib64/mysql/plugin/component_validate_password.so conflicts between attempted installs of community-mysql-server-8.0.17-2.fc30.x86_64 and mysql-community-server-8.0.17-1.fc30.x86_64 file /usr/lib64/mysql/plugin/connection_control.so conflicts between attempted installs of community-mysql-server-8.0.17-2.fc30.x86_64 and mysql-community-server-8.0.17-1.fc30.x86_64 file /usr/lib64/mysql/plugin/ddl_rewriter.so conflicts between attempted installs of community-mysql-server-8.0.17-2.fc30.x86_64 and mysql-community-server-8.0.17-1.fc30.x86_64 file /usr/lib64/mysql/plugin/group_replication.so conflicts between attempted installs of community-mysql-server-8.0.17-2.fc30.x86_64 and mysql-community-server-8.0.17-1.fc30.x86_64 file /usr/lib64/mysql/plugin/ha_example.so conflicts between attempted installs of community-mysql-server-8.0.17-2.fc30.x86_64 and mysql-community-server-8.0.17-1.fc30.x86_64 file /usr/lib64/mysql/plugin/ha_mock.so conflicts between attempted installs of community-mysql-server-8.0.17-2.fc30.x86_64 and mysql-community-server-8.0.17-1.fc30.x86_64 file /usr/lib64/mysql/plugin/innodb_engine.so conflicts between attempted installs of community-mysql-server-8.0.17-2.fc30.x86_64 and mysql-community-server-8.0.17-1.fc30.x86_64 file /usr/lib64/mysql/plugin/keyring_file.so conflicts between attempted installs of community-mysql-server-8.0.17-2.fc30.x86_64 and mysql-community-server-8.0.17-1.fc30.x86_64 file /usr/lib64/mysql/plugin/keyring_udf.so conflicts between attempted installs of community-mysql-server-8.0.17-2.fc30.x86_64 and mysql-community-server-8.0.17-1.fc30.x86_64 file /usr/lib64/mysql/plugin/libmemcached.so conflicts between attempted installs of community-mysql-server-8.0.17-2.fc30.x86_64 and mysql-community-server-8.0.17-1.fc30.x86_64 file /usr/lib64/mysql/plugin/locking_service.so conflicts between attempted installs of community-mysql-server-8.0.17-2.fc30.x86_64 and mysql-community-server-8.0.17-1.fc30.x86_64 file /usr/lib64/mysql/plugin/mypluglib.so conflicts between attempted installs of community-mysql-server-8.0.17-2.fc30.x86_64 and mysql-community-server-8.0.17-1.fc30.x86_64 file /usr/lib64/mysql/plugin/mysql_clone.so conflicts between attempted installs of community-mysql-server-8.0.17-2.fc30.x86_64 and mysql-community-server-8.0.17-1.fc30.x86_64 file /usr/lib64/mysql/plugin/mysql_no_login.so conflicts between attempted installs of community-mysql-server-8.0.17-2.fc30.x86_64 and mysql-community-server-8.0.17-1.fc30.x86_64 file /usr/lib64/mysql/plugin/rewrite_example.so conflicts between attempted installs of community-mysql-server-8.0.17-2.fc30.x86_64 and mysql-community-server-8.0.17-1.fc30.x86_64 file /usr/lib64/mysql/plugin/rewriter.so conflicts between attempted installs of community-mysql-server-8.0.17-2.fc30.x86_64 and mysql-community-server-8.0.17-1.fc30.x86_64 file /usr/lib64/mysql/plugin/semisync_master.so conflicts between attempted installs of community-mysql-server-8.0.17-2.fc30.x86_64 and mysql-community-server-8.0.17-1.fc30.x86_64 file /usr/lib64/mysql/plugin/semisync_slave.so conflicts between attempted installs of community-mysql-server-8.0.17-2.fc30.x86_64 and mysql-community-server-8.0.17-1.fc30.x86_64 file /usr/lib64/mysql/plugin/validate_password.so conflicts between attempted installs of community-mysql-server-8.0.17-2.fc30.x86_64 and mysql-community-server-8.0.17-1.fc30.x86_64 file /usr/lib64/mysql/plugin/version_token.so conflicts between attempted installs of community-mysql-server-8.0.17-2.fc30.x86_64 and mysql-community-server-8.0.17-1.fc30.x86_64 file /usr/sbin/mysqld conflicts between attempted installs of community-mysql-server-8.0.17-2.fc30.x86_64 and mysql-community-server-8.0.17-1.fc30.x86_64 file /var/lib/mysql conflicts between attempted installs of community-mysql-server-8.0.17-2.fc30.x86_64 and mysql-community-server-8.0.17-1.fc30.x86_64 file /var/lib/mysql-keyring conflicts between attempted installs of community-mysql-server-8.0.17-2.fc30.x86_64 and mysql-community-server-8.0.17-1.fc30.x86_64 file /usr/lib64/mysql/libmysqlclient.so.21.1.17 conflicts between attempted installs of community-mysql-libs-8.0.17-2.fc30.x86_64 and mysql-community-libs-8.0.17-1.fc30.x86_64 |
Since I’m not sure what’s wrong or how to fix it, I’ve put it in my queue of things to get to later. However, when I figure it out I’ll update this blog page with the solution or work around. If anybody knows the fix and would like to share, please let me know.
I removed the pending update packages with the following command:
dnf clean packages |
Then, I simply installed pgadmin4
with the following command:
dnf -y install pgadmin4 |
Display detailed console log →
The pgadmin4
configuration instructions can be found for several Linux versions at Josphat Mutai’s Computing for Geeks web page. On Fedora 30, you need to do the following:
- Install, start, and enable Apache as the
httpd
service unless you already have done that. - Copy the
/etc/httpd/conf.d/pgadmin4.conf.sample
file to/etc/httpd/conf.d/pgadmin4.conf
, which is a new file. - Restart the
httpd
service to incorporate thepgadmin4
configuration file.
After that, you create the following new directories as the root
or sudo
user:
/var/lib/pgadmin4
/var/log/pgadmin4
You can make both directories with a single mkdir
command, like:
mkdir -p /var/lib/pgadmin4 /var/log/pgadmin4 |
As the root
or sudo
user, change the ownership of these two directories to the apache
user with the following syntax:
chown -R apache:apache /var/lib/pgadmin4 /var/log/pgadmin4 |
You add the following four statements to the config_distro.py
file in the /usr/lib/python3.7/site-packages/pgadmin4-web
directory as the root
or sudo
user:
LOG_FILE = '/var/log/pgadmin4/pgadmin4.log' SQLITE_PATH = '/var/lib/pgadmin4/pgadmin4.db' SESSION_DB_PATH = '/var/lib/pgadmin4/sessions' STORAGE_DIR = '/var/lib/pgadmin4/storage' |
You need to setup the pgadmin user with the following python3 command:
python3 /usr/lib/python3.7/site-packages/pgadmin4-web/setup.py |
Enter the following values, a real email address and a password twice:
NOTE: Configuring authentication for SERVER mode. Enter the email address and password to use for the initial pgAdmin user account: Email address: admin@example.com Password: your_password Retype password: your_password pgAdmin 4 - Application Initialisation ====================================== |
Assuming you have an enabled firewall, you need to issue the following two commands as the root
or sudo
user:
rirewall-cmd --permanent --add-service=http firewall-cmd --reload |
You invoke pgAdmin4 from within a browser window with the following URL for a stand alone workstation (for a workstation on a DNS network you would enter pgadmin.domain.domain_type
in lieu of localhost):
pgadmin/localhost/pgadmin4 |
You most likely will encounter an Internal Server Error, the recommended fix is reputed to be:
ausearch -c 'httpd' --raw | audit2allow -M my-httpd semodule -X 300 -i my-httpd.pp |
It didn’t work for me. At the end of the process, I have an Internal Server Error. It is something that I’ll try to fix next. The actual error message:
Internal Server Error The server encountered an internal error or misconfiguration and was unable to complete your request. Please contact the server administrator at root@localhost to inform them of the time this error occurred, and the actions you performed just before this error. More information about this error may be available in the server error log. |
If somebody figures out the last step before I do, that’s great. Let me and everybody else know the mystery.
On a positive note, the pgadmin4 package provided the psycopg2
library. I had looked for it as a psycopg2
package but it is in python3-psycopg2
package.
Django on Fedora 30
It seemed opportune to add Django to the Fedora 30 instance that I build and maintain for my students. Here are the instructions, which I developed with the prior Fedora 28/29 instructions.
- Check your Python3 installation with the following command:
python3 -V
It should return this but if it doesn’t you should install
python3
:Python 3.7.4
- Check whether
pip3
is installation by installing it when its not:sudo def -y install python3-php
It should return:
Last metadata expiration check: 0:44:52 ago on Tue 10 Sep 2019 11:02:33 AM MDT. Package python3-pip-19.0.3-3.fc30.noarch is already installed. Dependencies resolved. Nothing to do. Complete!
- Check whether
Django
is installation by installing it when its not withpip3
installation utility:sudo pip3 install --user Django
It should return the following if installed:
Requirement already satisfied: Django in /usr/lib/python3.7/site-packages (2.1.10) Requirement already satisfied: pytz in /usr/lib/python3.7/site-packages (from Django) (2018.5)
- Check your
django-admin
account location with thewhich
utility:which django-admin
It should return the following on Fedora 30 when installed:
/usr/bin/django-admin
- Create a Django test application with the
django-admin
utility by creating a project directory. My directory is a bit deep. For reference, it is:/home/student/Code/python/django/projects
Change to that projects directory, and run the following command:
django-admin startproject test_app
After that command change directory with the
cd
command into thetest_app
subdirectory in yourprojects
directory. Run the manage.py program with the following command:python3 manage.py migrate
You should see the following:
Operations to perform: Apply all migrations: admin, auth, contenttypes, sessions Running migrations: Applying contenttypes.0001_initial... OK Applying auth.0001_initial... OK Applying admin.0001_initial... OK Applying admin.0002_logentry_remove_auto_add... OK Applying admin.0003_logentry_add_action_flag_choices... OK Applying contenttypes.0002_remove_content_type_name... OK Applying auth.0002_alter_permission_name_max_length... OK Applying auth.0003_alter_user_email_max_length... OK Applying auth.0004_alter_user_username_opts... OK Applying auth.0005_alter_user_last_login_null... OK Applying auth.0006_require_contenttypes_0002... OK Applying auth.0007_alter_validators_add_error_messages... OK Applying auth.0008_alter_user_username_max_length... OK Applying auth.0009_alter_user_last_name_max_length... OK Applying sessions.0001_initial... OK
Next, your would create an admin
account. You’re done.
Python MySQL Query
Somebody asked me how to expand a prior example with the static variables so that it took arguments at the command line for the variables. This example uses Python 3 new features in the datetime
package.
There’s a small trick converting the string
arguments to date
data types. Here’s a quick example that shows you how to convert the argument list into individual date
data type variables:
#!/usr/bin/python3 # include standard modules import sys from datetime import datetime # Capture argument list. fullCmdArguments = sys.argv # Assignable variables. beginDate = "" endDate = "" # Assign argument list to variable. argumentList = fullCmdArguments[1:] # Enumerate through the argument list where beginDate precedes endDate as strings. try: for i, s in enumerate(argumentList): if (i == 0): beginDate = datetime.date(datetime.fromisoformat(s)) elif (i == 1): endDate = datetime.date(datetime.fromisoformat(s)) except ValueError: print("One of the first two arguments is not a valid date (YYYY-MM-DD).") # Print the processed values and types. print("Begin Date: [",beginDate,"][",type(beginDate),"]") print("End Date: [",endDate,"][",type(endDate),"]") |
Assume you call this arguments.py
. Then, you call it with valid conforming date format value like the following command-line example:
./arguments.py 2001-01-01 2003-12-31 |
It returns the arguments after they have been converted to date
data types. The results should look like this:
Begin Date: 1991-01-01 [ <class 'datetime.date'> ] End Date: 2004-12-31 [ <class 'datetime.date'> ] |
The next Python example accepts dynamic arguments at the command line to query the MySQL database:
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 | #!/usr/bin/python3 # Import the library. import sys import mysql.connector from datetime import datetime from datetime import date from mysql.connector import errorcode # Capture argument list. fullCmdArguments = sys.argv # Assignable variables. start_date = "" end_date = "" # Assign argument list to variable. argumentList = fullCmdArguments[1:] # Check and process argument list. # ============================================================ # If there are less than two arguments provide default values. # Else enumerate and convert strings to dates. # ============================================================ if (len(argumentList) < 2): # Set a default start date. if (isinstance(start_date,str)): start_date = date(1980, 1, 1) # Set the default end date. if (isinstance(end_date,str)): end_date = datetime.date(datetime.today()) else: # Enumerate through the argument list where beginDate precedes endDate as strings. try: for i, s in enumerate(argumentList): if (i == 0): start_date = datetime.date(datetime.fromisoformat(s)) elif (i == 1): end_date = datetime.date(datetime.fromisoformat(s)) except ValueError: print("One of the first two arguments is not a valid date (YYYY-MM-DD).") # Attempt the query. # ============================================================ # Use a try-catch block to manage the connection. # ============================================================ try: # Open connection. cnx = mysql.connector.connect(user='student', password='student', host='127.0.0.1', database='studentdb') # Create cursor. cursor = cnx.cursor() # Set the query statement. query = ("SELECT CASE " " WHEN item_subtitle IS NULL THEN item_title " " ELSE CONCAT(item_title,': ',item_subtitle) " " END AS title, " "release_date " "FROM item " "WHERE release_date BETWEEN %s AND %s " "ORDER BY item_title") # Execute cursor. cursor.execute(query, (start_date, end_date)) # Display the rows returned by the query. for (item_name, release_date) in cursor: print("{}, {:%d-%b-%Y}".format(item_name, release_date)) # Handle exception and close connection. # ============================================================ except mysql.connector.Error as e: if e.errno == errorcode.ER_ACCESS_DENIED_ERROR: print("Something is wrong with your user name or password") elif e.errno == errorcode.ER_BAD_DB_ERROR: print("Database does not exist") else: print("Error code:", e.errno) # error number print("SQLSTATE value:", e.sqlstate) # SQLSTATE value print("Error message:", e.msg) # error message # Close the connection when the try block completes. finally: cnx.close() |
You can call the python-mysql-query.py
program with the following syntax:
./python-mysql-query.py 2001-01-01 2003-12-31 |
It returns the films between 1 Jan 2001 and 31 Dec 2003, like this:
Clear and Present Danger: Special Collector's Edition, 06-May-2003 Die Another Day: 2-Disc Ultimate Version, 03-Jun-2003 Die Another Day, 03-Jun-2003 Die Another Day, 03-Jun-2003 Golden Eye, 03-Jun-2003 Golden Eye: Special Edition, 03-Jun-2003 Harry Potter and the Chamber of Secrets, 28-May-2002 Harry Potter and the Chamber of Secrets: Two-Disc Special Edition, 28-May-2002 Harry Potter and the Sorcerer's Stone, 28-May-2002 Harry Potter and the Sorcerer's Stone: Two-Disc Special Edition, 28-May-2002 Harry Potter and the Sorcerer's Stone: Full Screen Edition, 28-May-2002 MarioKart: Double Dash, 17-Nov-2003 Pirates of the Caribbean, 30-Jun-2003 RoboCop, 24-Jul-2003 Splinter Cell: Chaos Theory, 08-Apr-2003 Star Wars II: Attack of the Clones, 16-May-2002 Star Wars II: Attack of the Clones, 16-May-2002 The Chronicles of Narnia: The Lion, the Witch and the Wardrobe, 30-Jun-2003 The Chronicles of Narnia: The Lion, the Witch and the Wardrobe, 16-May-2002 |
As always, I hope this helps somebody who wants to learn how to use Python with the MySQL database.
MySQL Python Connector
While building my student image on Fedora 30, I installed the MySQL PHP Connector (php-mysqlndrp) but neglected to install the Python Connector. This adds the installation and basic test of the Python Connector to the original blog post.
You use the following command with a wildcard as a privileged user. The wildcard is necessary because you need to load two libraries to support Python 2.7 and 3.7, which are installed on Fedora 30. You also need to be the root user or a user that is found in the sudoer’s list:
yum install -y mysql-connector-python* |
Display detailed console log →
Last metadata expiration check: 0:35:46 ago on Tue 20 Aug 2019 05:36:29 PM MDT. Dependencies resolved. ===================================================================================================================================== Package Architecture Version Repository Size ===================================================================================================================================== Installing: mysql-connector-python x86_64 8.0.17-1.fc30 mysql-connectors-community 435 k mysql-connector-python-cext x86_64 8.0.17-1.fc30 mysql-connectors-community 7.7 M mysql-connector-python3 x86_64 8.0.17-1.fc30 mysql-connectors-community 429 k mysql-connector-python3-cext x86_64 8.0.17-1.fc30 mysql-connectors-community 7.7 M Installing dependencies: python2-protobuf noarch 3.6.1-3.fc30 fedora 563 k python3-protobuf noarch 3.6.1-3.fc30 fedora 568 k Transaction Summary ===================================================================================================================================== Install 6 Packages Total download size: 17 M Installed size: 89 M Downloading Packages: (1/6): python3-protobuf-3.6.1-3.fc30.noarch.rpm 1.0 MB/s | 568 kB 00:00 (2/6): python2-protobuf-3.6.1-3.fc30.noarch.rpm 994 kB/s | 563 kB 00:00 (3/6): mysql-connector-python-8.0.17-1.fc30.x86_64.rpm 481 kB/s | 435 kB 00:00 (4/6): mysql-connector-python3-8.0.17-1.fc30.x86_64.rpm 612 kB/s | 429 kB 00:00 (5/6): mysql-connector-python-cext-8.0.17-1.fc30.x86_64.rpm 3.8 MB/s | 7.7 MB 00:02 (6/6): mysql-connector-python3-cext-8.0.17-1.fc30.x86_64.rpm 4.2 MB/s | 7.7 MB 00:01 ------------------------------------------------------------------------------------------------------------------------------------- Total 5.4 MB/s | 17 MB 00:03 warning: /var/cache/dnf/mysql-connectors-community-8bcc2bd350b53f70/packages/mysql-connector-python-8.0.17-1.fc30.x86_64.rpm: Header V3 DSA/SHA1 Signature, key ID 5072e1f5: NOKEY MySQL Connectors Community 7.0 MB/s | 27 kB 00:00 Importing GPG key 0x5072E1F5: Userid : "MySQL Release Engineering <mysql-build@oss.oracle.com>" Fingerprint: A4A9 4068 76FC BD3C 4567 70C8 8C71 8D3B 5072 E1F5 From : /etc/pki/rpm-gpg/RPM-GPG-KEY-mysql Key imported successfully Running transaction check Transaction check succeeded. Running transaction test Transaction test succeeded. Running transaction Preparing : 1/1 Installing : python3-protobuf-3.6.1-3.fc30.noarch 1/6 Installing : python2-protobuf-3.6.1-3.fc30.noarch 2/6 Installing : mysql-connector-python-8.0.17-1.fc30.x86_64 3/6 Installing : mysql-connector-python3-8.0.17-1.fc30.x86_64 4/6 Installing : mysql-connector-python3-cext-8.0.17-1.fc30.x86_64 5/6 Installing : mysql-connector-python-cext-8.0.17-1.fc30.x86_64 6/6 Running scriptlet: mysql-connector-python-cext-8.0.17-1.fc30.x86_64 6/6 Verifying : python2-protobuf-3.6.1-3.fc30.noarch 1/6 Verifying : python3-protobuf-3.6.1-3.fc30.noarch 2/6 Verifying : mysql-connector-python-8.0.17-1.fc30.x86_64 3/6 Verifying : mysql-connector-python-cext-8.0.17-1.fc30.x86_64 4/6 Verifying : mysql-connector-python3-8.0.17-1.fc30.x86_64 5/6 Verifying : mysql-connector-python3-cext-8.0.17-1.fc30.x86_64 6/6 Installed: mysql-connector-python-8.0.17-1.fc30.x86_64 mysql-connector-python-cext-8.0.17-1.fc30.x86_64 mysql-connector-python3-8.0.17-1.fc30.x86_64 mysql-connector-python3-cext-8.0.17-1.fc30.x86_64 python2-protobuf-3.6.1-3.fc30.noarch python3-protobuf-3.6.1-3.fc30.noarch Complete! |
Leveraging the MySQL Connector/Python Coding Examples documentation, Section 5.1 Connecting to MySQL Using Connector/Python here’s a test of the connection to MySQL 8.
# Import the library. import mysql.connector from mysql.connector import errorcode try: # Open connection. cnx = mysql.connector.connect(user='student', password='student', host='127.0.0.1', database='studentdb') # Print the value. print("Database connection resolved.") # Handle exception and close connection. except mysql.connector.Error as e: if e.errno == errorcode.ER_ACCESS_DENIED_ERROR: print("Something is wrong with your user name or password") elif e.errno == errorcode.ER_BAD_DB_ERROR: print("Database does not exist") else: print(e) # Close the connection when the try block completes. else: cnx.close() |
Leveraging the MySQL Connector/Python Coding Examples documentation, Section 5.4 Querying Data Using Connector/Python here’s a test of the connection to MySQL 8.
# Import the library. import datetime import mysql.connector from mysql.connector import errorcode try: # Open connection. cnx = mysql.connector.connect(user='student', password='student', host='127.0.0.1', database='studentdb') # Create cursor. cursor = cnx.cursor() # Set the query statement. query = ("SELECT " "CASE " " WHEN item_subtitle IS NULL THEN item_title " " ELSE CONCAT(item_title,': ',item_subtitle) " "END AS title, " "release_date " "FROM item " "WHERE release_date BETWEEN %s AND %s " "ORDER BY item_title") # Set the start and end date. start_date = datetime.date(1991, 1, 1) end_date = datetime.date(2004, 12, 31) # Execute cursor. cursor.execute(query, (start_date, end_date)) # Display the rows returned by the query. for (item_name, release_date) in cursor: print("{}, {:%d %b %Y}".format(item_name, release_date)) # Close cursor. cursor.close() # ------------------------------------------------------------ # Handle exception and close connection. except mysql.connector.Error as e: if e.errno == errorcode.ER_ACCESS_DENIED_ERROR: print("Something is wrong with your user name or password") elif e.errno == errorcode.ER_BAD_DB_ERROR: print("Database does not exist") else: print "Error code:", e.errno # error number print "SQLSTATE value:", e.sqlstate # SQLSTATE value print "Error message:", e.msg # error message # Close the connection when the try block completes. else: cnx.close() |
If you run the above in Python 2.7 it works fine. It fails to parse successfully in Python 3.x because the print()
function requires the parentheses all the time. You would need to re-write the except
block, like this with the parentheses:
# Handle exception and close connection. except mysql.connector.Error as e: if e.errno == errorcode.ER_ACCESS_DENIED_ERROR: print("Something is wrong with your user name or password") elif e.errno == errorcode.ER_BAD_DB_ERROR: print("Database does not exist") else: print("Error code:", e.errno) # error number print("SQLSTATE value:", e.sqlstate) # SQLSTATE value print("Error message:", e.msg) # error message |
While it works without the parentheses in Python 2.7, it also works with the parentheses. That means the best practice is to write cross compatible code by always using the parentheses with the print()
function.
As always, I hope this helps somebody.j