Performing PostgreSQL query
when searching from two lists for matches in a database i receive the following error:
ProgrammingError: operator does not exist: character varying ~~ text[]
LINE 1: ...FROM public."Phosphosite_table" WHERE "GENE_NAME" LIKE ARRAY...
^
HINT: No operator matches the given name and argument type(s). You might need to add explicit type casts.
my code is the following:
start = time.time()
input_file = "az20.tsv"
names = []
residuelist = []
kinase = []
fclist = []
with open(input_file, "r") as data:
data = csv.reader(data, delimiter='\t')
next(data, None)
for row in data:
data = row[0:6]
if "(" in data[0]:
name = data[0].split("(")[0]
residue1 = data[0].split("(")[1]
residue = residue1.split(")")[0]
fc = data[3]
else:
pass
if "_" in name:
name = name.split("_")[0]
if residue != "None":
names.append(str(name))
residuelist.append(str(residue))
fclist.append(fc)
genename = names
location = residuelist
connection = pg.connect(HAHAHA)
cur = connection.cursor()
cur.execute('SELECT "KINASE_NAME" FROM public."Phosphosite_table" WHERE "GENE_NAME" LIKE %s and "RESIDUE" LIKE %s',\
(genename, location))
query = cur.fetchall()
print query
connection.close()
end = time.time()
print str((end - start)/60) + " Minutes"
I have done some research and it appears that PostgreSQL does not perform any typecasting. However, I thought it would be a comparison of a string against a string, which, I changed before appending to my list. Does anyone have any advice?
Connor
However, I thought it would be a comparison of a string against a string
The part character varying ~~ text[] of the error message tells you, that you are comparing a string ("character varying") with an array ("text[]").
If you want to compare a single value with all elements of an array you need to use the ANY operator:
WHERE "GENE_NAME" LIKE any(%s)
assuming that %s is passed as native Postgres array from your code (which seems to be the case given the error message).
Related
My input strings are
inputData = "99998UNKNOWN"
inputData = "01000AMEBACIDE/TRICHOM/ANTIBAC 1"
inputData = "34343AMEBACIDE/TRICHOM/ANTIBACSADWA1"
ID = inputData.Substring(0,5);
Name = inputData.Substring(5,30);
Level = inputData.Substring(35,1);
I am getting the below error,
Index and length must refer to a location within the string.
I can understand , the error is due to the length that specified in substring for "Name" is not matching with first input.
Is there any way to handle this issue with any input length?
One approach is to add a "sentinel" suffix to the end of the string before taking substrings. Now you can add it to the data string before taking substrings from it. As long as the suffix has sufficient length, you would never get an index/length exception:
var padded = inputData.PadRight(32);
ID = padded.Substring(0, 5).Trim();
Name = padded.Substring(5, 30).Trim();
Level = padded.Substring(30, 1).Trim();
However, now your code should check if ID, Name, or Level is empty.
I am trying to get ask the user to input data in to perform the insert, it works whenever I have numbers, but when I input letters it gives me the error "LettersUsed" is not defined. I tried converting the input to str(input('Whatever')) but that did not do the trick any help why it does this?
import pymongo
import sys
#get a connection to database
connection = pymongo.MongoClient('mongodb://localhost')
#get a handle to database
db=connection.test
vehicles=db.vehicles
vehicle_VIN = input('What is the Vehicle VIN number? ')
vehicle_Make = input('What is the Vehicle Make? ')
newVehicle = {'VIN' : (vehicle_VIN).upper(), 'Make' : (vehicle_Make)}
try:
vehicles.insert_one(newVehicle)
print ('New Vehicle Inserted')
except Exception as e:
print 'Unexpected error:', type(e), e
#print Results
results = vehicles.find()
print()
# display documents in collection
for record in results:
print(record['VIN'] + ',',record['Make'])
#close the connection to MongoDB
connection.close()
Message: name 'DAFEQF' is not defined
In Python 2 the code input() is equal to eval(raw_input(prompt)). This means that whatever input you enter, Python2 tries to "evaluate" that input, and will complain that your input is not defined.
Make sure you replace input() with raw_input() (this is only for Python2!)
Replace
vehicle_VIN = input('What is the Vehicle VIN number? ')
vehicle_Make = input('What is the Vehicle Make? ')
with
vehicle_VIN = raw_input('What is the Vehicle VIN number? ')
vehicle_Make = raw_input('What is the Vehicle Make? ')
I am trying the following:
from pandas.io.sql import get_schema
tbl_schema = get_schema(contracts, 'my_contracts', keys=['country', 'contract_id'], con=db_engine)
I am getting this
ArgumentError: Element ['country', 'contract_id'] is not a string name or column element
which seems likely coming from this:
def _to_schema_column_or_string(element):
if hasattr(element, '__clause_element__'):
element = element.__clause_element__()
if not isinstance(element, util.string_types + (ColumnElement, )):
msg = "Element %r is not a string name or column element"
raise exc.ArgumentError(msg % element)
return element
I am not sure I understand how the multiple primary keys should be formatted to be parsed properly. I don't really understand this: util.string_types + (ColumnElement, ) I was hoping I could just point to the frame columns without having to define the whole SQLAlchemy schema.
Hi need help in using regexp for condition matching.
ex.my file has the following content
{hello.program='function'`;
bye.program='script'; }
I am trying to use regexp to match the string that has .program='function' in them:
pattern = '[.program]+\=(function)'
also tried pattern='[^\n]*(.hello=function)[^\n]*';
pattern_match = regexp(myfilename,pattern , 'match')
but this returns me pattern_match={} while i expect the result to be hello.program='function'`;
If 'function' comes with string-markers, you need to include these in the match. Also, you need to escape the dot (otherwise, it's considered "any character"). [.program]+ looks for one or several letters contained in the square brackets - but you can just look for program instead. Also, you don't need to escape the =-sign (which is probably what messed up the match).
cst = {'hello.program=''function''';'bye.program=''script'''; };
pat = 'hello\.program=''function''';
out = regexp(cst,pat,'match');
out{1}{1} %# first string from list, first match
hello.program='function'
EDIT
In response to the comment
my file contains
m2 = S.Parameter;
m2.Value = matlabstandard;
m2.Volatility = 'Tunable';
m2.Configurability = 'None';
m2.ReferenceInterfaceFile ='';
m2.DataType = 'auto';
my objective is to find all the lines that match, .DataType='auto'
Here's how you find the matching lines with regexp
%# read the file with textscan into a variable txt
fid = fopen('myFile.m');
txt = textscan(fid,'%s');
fclose(fid);
txt = txt{1};
%# find the match. Allow spaces and equal signs between DataType and 'auto'
match = regexp(txt,'\.DataType[ =]+''auto''','match')
%# match is not empty only if a match was found. Identify the non-empty match
matchedLine = find(~cellfun(#isempty,match));
Try this as it matches .program='function' exactly:
(\.)program='function'
I think this did not work:
'[.program]+\=(function)'
because of how the []'s work. Here is a link explaining why I say that: http://www.regular-expressions.info/charclass.html
my code:
String [] temp;
temp = {"one","two","three"};
I get this error:
Illegal start of expression, ';' expected.
Curly braces, the way you have used them, can only be used in array declaration statements. i.e.
String[] temp = {"one","two","three"};