Develop Reference

Postgres: invalid input syntax for type date

I have created a database and I am trying to fetch data from it. I have a class Query and inside the class I have a function that calls a table called forecasts. The function is as follows:
def forecast(self, provider: str, zone: str='Mainland',):
self.date_start = date_start)
self.date_end = (date_end)
self.df_forecasts = pd.DataFrame()
fquery = """
SELECT dp.name AS provider_name, lf.datetime_from AS date, fr.name AS run_name, lf.value AS value
FROM load_forecasts lf
INNER JOIN bidding_zones bz ON lf.zone_id = bz.zone_id
INNER JOIN data_providers dp ON lf.provider_id = dp.provider_id
INNER JOIN forecast_runs fr ON lf.run_id = fr.run_id
WHERE bz.name = '{zone}'
AND dp.name = '{provider}'
AND date(lf.datetime_from) BETWEEN '{self.date_start}' AND '{self.date_end}'
"""
df_forecasts = pd.read_sql_query(fquery, self.connection)
return df_forecasts
In the scripts that I run I am calling the Query class giving it my inputs
query = Query(date_start, date_end)
And the function
forecast_df = query.forecast(provider='Meteologica')
I run my script in the command line in the classic way
python myscript.py '2022-11-10' '2022-11-18'
My script shows the error
sqlalchemy.exc.DataError: (psycopg2.errors.InvalidDatetimeFormat) invalid input syntax for type date: "{self.date_start}"
LINE 9: AND date(lf.datetime_from) BETWEEN '{self.date_start...
when I use this syntax, but when I manually input the string for date_start and date_end it works.

I cannot find a way to solve the problem with sqlalchemy, so I opened a cursor with psycopg2.
# Returns the datetime, value and provider name and issue date of the forecasts in the load_forecasts table
# The dates range is specified by the user when the class is called
def forecast(self, provider: str, zone: str='Mainland',):
# Opens a cursor to get the data
cursor = self.connection.cursor()
# Query to run
query = """
SELECT dp.name, lf.datetime_from, fr.name, lf.value, lf.issue_date
FROM load_forecasts lf
INNER JOIN bidding_zones bz ON lf.zone_id = bz.zone_id
INNER JOIN data_providers dp ON lf.provider_id = dp.provider_id
INNER JOIN forecast_runs fr ON lf.run_id = fr.run_id
WHERE bz.name = %s
AND dp.name = %s
AND date(lf.datetime_from) BETWEEN %s AND %s
"""
# Execute the query, bring the data and close the cursor
cursor.execute(query, (zone, provider, self.date_start, self.date_end))
self.df_forecasts = cursor.fetchall()
cursor.close()
return self.df_forecasts
If anyone finds the answer with sqlalchemy, I would love to see it!

How change one value to another in one place and use it in couple functions?

I'm writing test automation for API in BDD behave. I need a switcher between environments. Is any possible way to change one value in one place without adding this value to every functions? Example:
I've tried to do it by adding value to every function but its makes all project very complicated
headers = {
'Content-Type': 'application/json',
'country': 'fi'
}
what i what to switch only country value in headers e.g from 'fi' to 'es'
and then all function should switch themselves to es environment, e.g
def sending_post_request(endpoint, user):
url = fi_api_endpoints.api_endpoints_list.get(endpoint)
personalId = {'personalId': user}
json_post = requests.post(url,
headers=headers,
data=json.dumps(personalId)
)
endpoint_message = json_post.text
server_status = json_post.status_code
def phone_number(phone_number_status):
if phone_number_status == 'wrong':
cursor = functions_concerning_SQL_conection.choosen_db('fi_sql_identity')
cursor.execute("SELECT TOP 1 PersonalId from Registrations where PhoneNumber is NULL")
result = cursor.fetchone()
user_with_no_phone_number = result[0]
return user_with_no_phone_number
else:
cursor = functions_concerning_SQL_conection.choosen_db('fi_sql_identity')
cursor.execute("SELECT TOP 1 PersonalId from Registrations where PhoneNumber is not NULL")
result = cursor.fetchone()
user_with_phone_number = result[0]
return user_with_phone_number
and when i will change from 'fi' to 'es' in headers i want:
fi_sql_identity change to es_sql_identity
url = fi_api_endpoints.api_endpoints_list.get(endpoint) change to
url = es_api_endpoints.api_endpoints_list.get(endpoint)
thx and please help

With respect to your original question, a solution for this case is closure:
def f(x):
def long_calculation(y):
return x * y
return long_calculation
# create different functions without dispatching multiple times
g = f(val_1)
h = f(val_2)
g(val_3)
h(val_3)
Well, the problem is why do you hardcode everything? With the update you can simplify your function as:
def phone_number(phone_number_status, db_name='fi_sql_identity'):
cursor = functions_concerning_SQL_conection.choosen_db(db_name)
if phone_number_status == 'wrong':
sql = "SELECT TOP 1 PersonalId from Registrations where PhoneNumber is NULL"
else:
sql = "SELECT TOP 1 PersonalId from Registrations where PhoneNumber is not NULL"
cursor.execute(sql)
result = cursor.fetchone()
return result[0]
Also please don't write like:
# WRONG
fi_db_conn.send_data()
But use a parameter:
region = 'fi' # or "es"
db_conn = initialize_conn(region)
db_conn.send_data()
And use a config file to store your endpoints with respect to your region, e.g. consider YAML:
# config.yml
es:
db_name: es_sql_identity
fi:
db_name: fi_sql_identity
Then use them in Python:
import yaml
with open('config.yml') as f:
config = yaml.safe_load(f)
region = 'fi'
db_name = config[region]['db_name'] # "fi_sql_identity"
# status = ...
result = phone_number(status, db_name)
See additional useful link for using YAML.

First, provide an encapsulation how to access the resources of a region by providing this encapsulation with a region parameter. It may also be a good idea to provide this functionality as a behave fixture.
CASE 1: region parameter needs to vary between features / scenarios
For example, this means that SCENARIO_1 needs region="fi" and SCENARIO_2 needs region="es".
Use fixture and fixture-tag with region parameter.
In this case you need to write own scenarios for each region (BAD TEST REUSE)
or use a ScenarioOutline as template to let behave generate the tests for you (by using a fixture-tag with a region parameter value for example).
CASE 2: region parameter is constant for all features / scenarios (during test-run)
You can support multiple test-runs with different region parameters by using a userdata parameter.
Look at behave userdata concept.
This allows you to run behave -D region=fi ... and behave -D region=es ...
This case provides a better reuse of testsuite, meaning a large part of the testsuite is the common testsuite that is applied to all regions.
HINT: Your code examples are too specific ("fi" based) which is a BAD-SMELL.

Why is Twisted's adbapi failing to recover data from within unittests?

Overview
Context
I am writing unit tests for some higher-order logic that depends on writing to an SQLite3 database. For this I am using twisted.trial.unittest and twisted.enterprise.adbapi.ConnectionPool.
Problem statement
I am able to create a persistent sqlite3 database and store data therein. Using sqlitebrowser, I am able to verify that the data has been persisted as expected.
The issue is that calls to t.e.a.ConnectionPool.run* (e.g.: runQuery) return an empty set of results, but only when called from within a TestCase.
Notes and significant details
The problem I am experiencing occurs only within Twisted's trial framework. My first attempt at debugging was to pull the database code out of the unit test and place it into an independent test/debug script. Said script works as expected while the unit test code does not (see examples below).
Case 1: misbehaving unit test
init.sql
This is the script used to initialize the database. There are no (apparent) errors stemming from this file.
CREATE TABLE ajxp_changes ( seq INTEGER PRIMARY KEY AUTOINCREMENT, node_id NUMERIC, type TEXT, source TEXT, target TEXT, deleted_md5 TEXT );
CREATE TABLE ajxp_index ( node_id INTEGER PRIMARY KEY AUTOINCREMENT, node_path TEXT, bytesize NUMERIC, md5 TEXT, mtime NUMERIC, stat_result BLOB);
CREATE TABLE ajxp_last_buffer ( id INTEGER PRIMARY KEY AUTOINCREMENT, type TEXT, location TEXT, source TEXT, target TEXT );
CREATE TABLE ajxp_node_status ("node_id" INTEGER PRIMARY KEY NOT NULL , "status" TEXT NOT NULL DEFAULT 'NEW', "detail" TEXT);
CREATE TABLE events (id INTEGER PRIMARY KEY AUTOINCREMENT, type text, message text, source text, target text, action text, status text, date text);
CREATE TRIGGER LOG_DELETE AFTER DELETE ON ajxp_index BEGIN INSERT INTO ajxp_changes (node_id,source,target,type,deleted_md5) VALUES (old.node_id, old.node_path, "NULL", "delete", old.md5); END;
CREATE TRIGGER LOG_INSERT AFTER INSERT ON ajxp_index BEGIN INSERT INTO ajxp_changes (node_id,source,target,type) VALUES (new.node_id, "NULL", new.node_path, "create"); END;
CREATE TRIGGER LOG_UPDATE_CONTENT AFTER UPDATE ON "ajxp_index" FOR EACH ROW BEGIN INSERT INTO "ajxp_changes" (node_id,source,target,type) VALUES (new.node_id, old.node_path, new.node_path, CASE WHEN old.node_path = new.node_path THEN "content" ELSE "path" END);END;
CREATE TRIGGER STATUS_DELETE AFTER DELETE ON "ajxp_index" BEGIN DELETE FROM ajxp_node_status WHERE node_id=old.node_id; END;
CREATE TRIGGER STATUS_INSERT AFTER INSERT ON "ajxp_index" BEGIN INSERT INTO ajxp_node_status (node_id) VALUES (new.node_id); END;
CREATE INDEX changes_node_id ON ajxp_changes( node_id );
CREATE INDEX changes_type ON ajxp_changes( type );
CREATE INDEX changes_node_source ON ajxp_changes( source );
CREATE INDEX index_node_id ON ajxp_index( node_id );
CREATE INDEX index_node_path ON ajxp_index( node_path );
CREATE INDEX index_bytesize ON ajxp_index( bytesize );
CREATE INDEX index_md5 ON ajxp_index( md5 );
CREATE INDEX node_status_status ON ajxp_node_status( status );
test_sqlite.py
This is the unit test class that fails unexpectedly. TestStateManagement.test_db_clean passes, indicated that the tables were properly created. TestStateManagement.test_inode_create fails, reporitng that zero results were retrieved.
import os.path as osp
from twisted.internet import defer
from twisted.enterprise import adbapi
import sqlengine # see below
class TestStateManagement(TestCase):
def setUp(self):
self.meta = mkdtemp()
self.db = adbapi.ConnectionPool(
"sqlite3", osp.join(self.meta, "db.sqlite"), check_same_thread=False,
)
self.stateman = sqlengine.StateManager(self.db)
with open("init.sql") as f:
script = f.read()
self.d = self.db.runInteraction(lambda c, s: c.executescript(s), script)
def tearDown(self):
self.db.close()
del self.db
del self.stateman
del self.d
rmtree(self.meta)
#defer.inlineCallbacks
def test_db_clean(self):
"""Canary test to ensure that the db is initialized in a blank state"""
yield self.d # wait for db to be initialized
q = "SELECT name FROM sqlite_master WHERE type='table' AND name=?;"
for table in ("ajxp_index", "ajxp_changes"):
res = yield self.db.runQuery(q, (table,))
self.assertTrue(
len(res) == 1,
"table {0} does not exist".format(table)
)
#defer.inlineCallbacks
def test_inode_create_file(self):
yield self.d
path = osp.join(self.ws, "test.txt")
with open(path, "wt") as f:
pass
inode = mk_dummy_inode(path)
yield self.stateman.create(inode, directory=False)
entry = yield self.db.runQuery("SELECT * FROM ajxp_index")
emsg = "got {0} results, expected 1. Are canary tests failing?"
lentry = len(entry)
self.assertTrue(lentry == 1, emsg.format(lentry))
sqlengine.py
These are the artefacts being tested by the above unit tests.
def values_as_tuple(d, *param):
"""Return the values for each key in `param` as a tuple"""
return tuple(map(d.get, param))
class StateManager:
"""Manages the SQLite database's state, ensuring that it reflects the state
of the filesystem.
"""
log = Logger()
def __init__(self, db):
self._db = db
def create(self, inode, directory=False):
params = values_as_tuple(
inode, "node_path", "bytesize", "md5", "mtime", "stat_result"
)
directive = (
"INSERT INTO ajxp_index (node_path,bytesize,md5,mtime,stat_result) "
"VALUES (?,?,?,?,?);"
)
return self._db.runOperation(directive, params)
Case 2: bug disappears outside of twisted.trial
#! /usr/bin/env python
import os.path as osp
from tempfile import mkdtemp
from twisted.enterprise import adbapi
from twisted.internet.task import react
from twisted.internet.defer import inlineCallbacks
INIT_FILE = "example.sql"
def values_as_tuple(d, *param):
"""Return the values for each key in `param` as a tuple"""
return tuple(map(d.get, param))
def create(db, inode):
params = values_as_tuple(
inode, "node_path", "bytesize", "md5", "mtime", "stat_result"
)
directive = (
"INSERT INTO ajxp_index (node_path,bytesize,md5,mtime,stat_result) "
"VALUES (?,?,?,?,?);"
)
return db.runOperation(directive, params)
def init_database(db):
with open(INIT_FILE) as f:
script = f.read()
return db.runInteraction(lambda c, s: c.executescript(s), script)
#react
#inlineCallbacks
def main(reactor):
meta = mkdtemp()
db = adbapi.ConnectionPool(
"sqlite3", osp.join(meta, "db.sqlite"), check_same_thread=False,
)
yield init_database(db)
# Let's make sure the tables were created as expected and that we're
# starting from a blank slate
res = yield db.runQuery("SELECT * FROM ajxp_index LIMIT 1")
assert not res, "database is not empty [ajxp_index]"
res = yield db.runQuery("SELECT * FROM ajxp_changes LIMIT 1")
assert not res, "database is not empty [ajxp_changes]"
# The details of this are not important. Suffice to say they (should)
# conform to the DB schema for ajxp_index.
test_data = {
"node_path": "/this/is/some/arbitrary/path.ext",
"bytesize": 0,
"mtime": 179273.0,
"stat_result": b"this simulates a blob of raw binary data",
"md5": "d41d8cd98f00b204e9800998ecf8427e", # arbitrary
}
# store the test data in the ajxp_index table
yield create(db, test_data)
# test if the entry exists in the db
entry = yield db.runQuery("SELECT * FROM ajxp_index")
assert len(entry) == 1, "got {0} results, expected 1".format(len(entry))
print("OK")
Closing remarks
Again, upon checking with sqlitebrowser, it seems as though the data is being written to db.sqlite, so this looks like a retrieval problem. From here, I'm sort of stumped... any ideas?
EDIT
This code will produce an inode that that can be used for testing.
def mk_dummy_inode(path, isdir=False):
return {
"node_path": path,
"bytesize": osp.getsize(path),
"mtime": osp.getmtime(path),
"stat_result": dumps(stat(path), protocol=4),
"md5": "directory" if isdir else "d41d8cd98f00b204e9800998ecf8427e",
}

Okay, it turns out that this is a bit of a tricky one. Running the tests in isolation (as was posted to this question) makes it such that the bug only rarely occurs. However, when running in the context of an entire test suite, it fails almost 100% of the time.
I added yield task.deferLater(reactor, .00001, lambda: None) after writing to the db and before reading from the db, and this solves the issue.
From there, I suspected this might be a race condition stemming from the connection pool and sqlite's limited concurrency-tolerance. I tried setting the cb_min and cb_max parameters to ConnectionPool to 1, and this also solved the issue.
In short: it seems as though sqlite doesn't play very nicely with multiple connections, and that the appropriate fix is to avoid concurrency to the extent possible.

If you take a look at your setUp function, you're returning self.db.runInteraction(...), which returns a deferred. As you've noted, you assume that it waits for the deferred to finish. However this is not the case and it's a trap that most fall victim to (myself included). I'll be honest with you, for situations like this, especially for unit tests, I just execute the synchronous code outside the TestCase class to initialize the database. For example:
def init_db():
import sqlite3
conn = sqlite3.connect('db.sqlite')
c = conn.cursor()
with open("init.sql") as f:
c.executescript(f.read())
init_db() # call outside test case
class TestStateManagement(TestCase):
"""
My test cases
"""
Alternatively, you could decorate the setup and yield runOperation(...) but something tells me that it wouldn't work... In any case, it's surprising that no errors were raised.
PS
I've been eyeballing this question for a while and it's been in the back of my head for days now. A potential reason for this finally dawned on me at nearly 1am. However, I'm too tired/lazy to actually test this out :D but it's a pretty damn good hunch. I'd like to commend you on your level of detail in this question.

Calling Argument in Python code

I have the following code that demands a -p argument when calling. However, how do I call the -p argument in the SQL query? I am also looking to use this -p argument text in the output file name.
#!/usr/bin/python
import argparse
import psycopg2
import csv
parser = argparse.ArgumentParser(description='insert the project ID as an
argument')
parser.add_argument('-p','--project_id', help='project_id to pull files from
ERAPRO',required=True)
args = parser.parse_args()
conn = psycopg2.connect(database="XXX", user="XXX", password="XXX",
host="XXX", port="5432")
cur = conn.cursor()
cur.execute("""SELECT project_analysis.project_accession,
analysis.analysis_accession, file.filename, file.file_md5, file.file_location
FROM project_analysis
LEFT JOIN analysis on project_analysis.analysis_accession = analysis.analysis_accession
LEFT JOIN analysis_file on analysis.analysis_accession = analysis_file.analysis_accession
LEFT JOIN file on analysis_file.file_id = file.file_id
WHERE project_accession = <INSERT -p ARGUMENT HERE> and analysis.hidden_in_eva = '0';""")
records = cur.fetchall()
with open ('/nfs/production3/eva/user/gary/evapro_ftp/<INSERT -p ARGUMENT
HERE>.csv', 'w') as f:
writer = csv.writer (f, delimiter = ',')
for row in records:
writer.writerow(row)
conn.close()
All help appreciated.
Thanks

First assign your argument to variable using dest argument to add_argument(). lets say we assign the input to the project_id variable.
This way we can reference it in the code.
parser.add_argument('-p','--project_id',
help='project_id to pull files from
ERAPRO',
required=True,
dest='project_id') # notice the dest argument
cur.execute("""SELECT project_analysis.project_accession,
analysis.analysis_accession, file.filename, file.file_md5, file.file_location
FROM project_analysis
LEFT JOIN analysis on project_analysis.analysis_accession = analysis.analysis_accession
LEFT JOIN analysis_file on analysis.analysis_accession = analysis_file.analysis_accession
LEFT JOIN file on analysis_file.file_id = file.file_id
WHERE project_accession = %s and analysis.hidden_in_eva = '0';""", (args.project_id))
Notice the use of execute(' ... %s ...', (args.project_id)) by doing this we interpolated the value referenced by project_id into the string.

After calling args = parser.parse_args() you can obtain the value of the arguments like this:
pid = args.project_id
Then you can use that value of pid in your code by using normal string substitution. However, it's better to use psycopg2's inbuilt method for passing parameters to SQL queries to prevent SQL injection.
Normal string substitution:
'hello world {]'.format(var_name)
psycopg2:
cur.execute('SELECT * from %s', (var_name))

Auto format arguments to string

I am writing a function that takes some arguments and builds a SQL query string. I currently have each of the keyword arguments assigned to the string by name, and I am thinking that there has to be an easier way to automatically format the keyword arguments expected in the string. I'm wondering if it is possible to automatically format (or assign) a keyword argument to the query string if the argument name matches.
Here is my current function:
def create_query(
who_id,
what_id=None,
owner_id=None,
subject,
description,
due_date,
is_closed=False,
is_priority=False,
is_reminder=True,
):
query_str = """
'WhoId':'{who_id}',
'Subject':'{subject}',
'Description':'{description}',
'ActivityDate':'{due_date}',
'IsClosed':'{is_closed}',
'IsPriority':'{is_priority}',
'IsReminderSet':'{is_reminder}',
""".format(
who_id=who_id,
subject=subject, # Mapping each of these to the
description=description, # identically named variable
due_date=due_date, # seems dumb
is_closed=is_closed,
is_priority=is_priority,
is_reminder=is_reminder,
)
And I would like something that is more like this:
def create_query(**kwargs):
query_string = """
'WhoId':'{who_id}',
'Subject':'{subject}',
'Description':'{description}',
...
""".format(
for key in **kwargs:
if key == << one of the {keyword} variables in query_string >>:
key = << the matching variable in query_string >>

def create_query(**kwargs):
query_string = """
'WhoId':'{who_id}',
'Subject':'{subject}',
'Description':'{description}',
...
""".format(**kwargs)
print(query_string)
Can be used like this then:
create_query(who_id=123, subject="Boss", description="he's bossy",
will_be_ignored="really?")
Prints:
'WhoId':'123',
'Subject':'Boss',
'Description':'he is bossy',
...
Note the additional parameter will_be_ignored that I entered. It will simply be ignored. You don't have to filter that yourself.
But better don't build the query string yourself. Let the database connector handle that. For example, if my example said "he's bossy" then that would break the query because it uses ' as delimiter. Your database connector should allow you to give it queries with placeholders and values, and then properly replace the placeholders with the values.
Alternative:
def create_query(**kwargs):
parameters = (('WhoId', 'who_id'),
('Subject','subject'),
('Description', 'description'))
query_string = ','.join(r"'{}':'{{{}}}'".format(name, kwargs[id])
for name, id in parameters
if id in kwargs)
print(query_string)
create_query(who_id=123, description="he's bossy",
will_be_ignored="really?")
Prints:
'WhoId':'{123}','Description':'{he's bossy}'