Develop Reference

Python variable substitution

I have a script that calls a list of linux guests I am trying to tidy up. Here is the code:
#!/usr/bin/python
guests = ['guest1','guest2','guest3','guest*']
def serverCheck(guestList)
for g in guestList:
server = AdminControl.completeObjectName('cell=tstenvironment,node=guest1,name=uatenvironment,type=Server,*')
try:
status = AdminControl.getAttribute(server, 'state')
print g + status
except:
print "Error %s is down." % g
serverCheck(guests)
The problem lies in this line:
server = AdminControl.completeObjectName('cell=Afcutst,node=%s,name=afcuuat1,type=Server,*') % g
How do I use my list to populate the node variable while still being able to pass the info within the parentheses to the AdminControl function?

The argument string itself is the argument to the % operator, not the return value of the function call.
server = AdminControl.completeObjectName(
'cell=Afcutst,node=%s,name=afcuuat1,type=Server,*' % (g,)
)
Peeking into the crystal ball, Python 3.6 will allow you to write
server = AdminControl.completeObjectName(
f'cell=Afcutst,node={g},name=afcuuat1,type=Server,*'
)
embedding the variable directly into a special format string literal.

can you try like this
AdminControl.completeObjectName('cell=tstenvironment,node=%s,name=uatenvironment,type=Server,*'%g)

For more readability I would suggest this and also using the same way to format strings from variables (here I chose str.format)
guests = ['guest1','guest2','guest3','guest*']
def serverCheck(guestList)
name_tpl = 'cell=tstenvironment,node={},name=uatenvironment,type=Server,*'
for g in guestList:
obj_name = name_tpl.format(g)
server = AdminControl.completeObjectName(obj_name)
try:
status = AdminControl.getAttribute(server, 'state')
print '{}: {}'.format(g, status)
except:
print 'Error {} is down'.format(g)
serverCheck(guests)

Input parameter instead of using raw_input to write python function

we are writing a def. here is our logic:
input table's field name,
input parameter to the parentheses(parentheses is set for some commands who needs to input string such as:
interface fa(1)/(2)
ip address (3) (4))
input parameter to the parentheses (if requested),then will select command from sqlite db.
interface fa0/1
ip address 192.168.1.1 255.255.255.0
Finally output commands.
Recently, my partner requests me that I have not to use input. He told me that I should use "input parameter". And I didn't understand him and he is not responding me about this question.
I have no idea now. What does it mean?
This is my and my partners python codes:
def get_input():
a = input("function and params (comma separated):")
b = input("device:")
pattern = re.compile('\(.*?\)')
output_commands = []
params = a.split(',')
function = params[0]
print (params)
counter = 1
for result in readciscodevice(function,b):
command = result[0]
found_parentheses_list = re.findall(pattern, command)
output_command = command
for i, param_placeholder in enumerate(found_parentheses_list):
param = params[counter]
output_command = re.sub(pattern, param, output_command, count=1)
counter +=1
output_commands.append(output_command)
return output_commands
# other program calls:
commands = get_input()
for command in commands:
#do sth, print for example
print(command)

Creating loop for __main__

I am new to Python, and I want your advice on something.
I have a script that runs one input value at a time, and I want it to be able to run a whole list of such values without me typing the values one at a time. I have a hunch that a "for loop" is needed for the main method listed below. The value is "gene_name", so effectively, i want to feed in a list of "gene_names" that the script can run through nicely.
Hope I phrased the question correctly, thanks! The chunk in question seems to be
def get_probes_from_genes(gene_names)
import json
import urllib2
import os
import pandas as pd
api_url = "http://api.brain-map.org/api/v2/data/query.json"
def get_probes_from_genes(gene_names):
if not isinstance(gene_names,list):
gene_names = [gene_names]
#in case there are white spaces in gene names
gene_names = ["'%s'"%gene_name for gene_name in gene_names]**
api_query = "?criteria=model::Probe"
api_query= ",rma::criteria,[probe_type$eq'DNA']"
api_query= ",products[abbreviation$eq'HumanMA']"
api_query= ",gene[acronym$eq%s]"%(','.join(gene_names))
api_query= ",rma::options[only$eq'probes.id','name']"
data = json.load(urllib2.urlopen(api_url api_query))
d = {probe['id']: probe['name'] for probe in data['msg']}
if not d:
raise Exception("Could not find any probes for %s gene. Check " \
"http://help.brain- map.org/download/attachments/2818165/HBA_ISH_GeneList.pdf? version=1&modificationDate=1348783035873 " \
"for list of available genes."%gene_name)
return d
def get_expression_values_from_probe_ids(probe_ids):
if not isinstance(probe_ids,list):
probe_ids = [probe_ids]
#in case there are white spaces in gene names
probe_ids = ["'%s'"%probe_id for probe_id in probe_ids]
api_query = "? criteria=service::human_microarray_expression[probes$in%s]"% (','.join(probe_ids))
data = json.load(urllib2.urlopen(api_url api_query))
expression_values = [[float(expression_value) for expression_value in data["msg"]["probes"][i]["expression_level"]] for i in range(len(probe_ids))]
well_ids = [sample["sample"]["well"] for sample in data["msg"] ["samples"]]
donor_names = [sample["donor"]["name"] for sample in data["msg"] ["samples"]]
well_coordinates = [sample["sample"]["mri"] for sample in data["msg"] ["samples"]]
return expression_values, well_ids, well_coordinates, donor_names
def get_mni_coordinates_from_wells(well_ids):
package_directory = os.path.dirname(os.path.abspath(__file__))
frame = pd.read_csv(os.path.join(package_directory, "data", "corrected_mni_coordinates.csv"), header=0, index_col=0)
return list(frame.ix[well_ids].itertuples(index=False))
if __name__ == '__main__':
probes_dict = get_probes_from_genes("SLC6A2")
expression_values, well_ids, well_coordinates, donor_names = get_expression_values_from_probe_ids(probes_dict.keys())
print get_mni_coordinates_from_wells(well_ids)

whoa, first things first. Python ain't Java, so do yourself a favor and use a nice """xxx\nyyy""" string, with triple quotes to multiline.
api_query = """?criteria=model::Probe"
,rma::criteria,[probe_type$eq'DNA']
...
"""
or something like that. you will get white spaces as typed, so you may need to adjust.
If, like suggested, you opt to loop on the call to your function through a file, you will need to either try/except your data-not-found exception or you will need to handle missing data without throwing an exception. I would opt for returning an empty result myself and letting the caller worry about what to do with it.
If you do opt for raise-ing an Exception, create your own, rather than using a generic exception. That way your code can catch your expected Exception first.
class MyNoDataFoundException(Exception):
pass
#replace your current raise code with...
if not d:
raise MyNoDataFoundException(your message here)
clarification about catching exceptions, using the accepted answer as a starting point:
if __name__ == '__main__':
with open(r"/tmp/genes.txt","r") as f:
for line in f.readlines():
#keep track of your input data
search_data = line.strip()
try:
probes_dict = get_probes_from_genes(search_data)
except MyNoDataFoundException, e:
#and do whatever you feel you need to do here...
print "bummer about search_data:%s:\nexception:%s" % (search_data, e)
expression_values, well_ids, well_coordinates, donor_names = get_expression_values_from_probe_ids(probes_dict.keys())
print get_mni_coordinates_from_wells(well_ids)

You may want to create a file with Gene names, then read content of the file and call your function in the loop. Here is an example below
if __name__ == '__main__':
with open(r"/tmp/genes.txt","r") as f:
for line in f.readlines():
probes_dict = get_probes_from_genes(line.strip())
expression_values, well_ids, well_coordinates, donor_names = get_expression_values_from_probe_ids(probes_dict.keys())
print get_mni_coordinates_from_wells(well_ids)

pass file path through cmd to python script

I am using vb.net and Arcobjects for my program. I am creating a button for ArcMap 10 that will convert a kml to a lyr file.
I am having problems passing variables into the python code. The variables are file paths and it works great if I hard code them in with / instead of . When the variables are dynamically passed in, the program breaks at the "/"s in the path names:
Dim Filelocation As OpenFileDialog = New OpenFileDialog()
Filelocation.Title = "Please point photo of the owner"
Filelocation.InitialDirectory = "B:\GeoSpatialData\Projects\004402 Griffiths\File Structure\Geospatial\GPS\KML"
If Filelocation.ShowDialog = DialogResult.OK Then
Dim kmlFile As String
kmlFile = Filelocation.FileName
Dim args As String
args = kmlFile & " " & kmlFile.Substring(0, kmlFile.LastIndexOf("\")) & " test"
Dim args2 As String = args.Replace("\", "/")
Dim procStartInfo As System.Diagnostics.ProcessStartInfo = New System.Diagnostics.ProcessStartInfo("C:\Python26\python", "C:\Users\KJacobsen\kml_to_shp.py " & args2)
' The following commands are needed to redirect the standard output.
' This means that it will be redirected to the Process.StandardOutput StreamReader.
procStartInfo.RedirectStandardOutput = True
procStartInfo.UseShellExecute = False
' Do not create the black window.
procStartInfo.CreateNoWindow = False
' Now you create a process, assign its ProcessStartInfo, and start it.
Dim proc As New System.Diagnostics.Process()
proc.StartInfo = procStartInfo
proc.Start()
proc.WaitForExit()
' Get the output into a string.
Dim result As String = proc.StandardOutput.ReadToEnd()
' Display the command output.
Console.WriteLine(result)
End If
Catch objException As Exception
' Log the exception and errors.
Console.WriteLine(objException.Message)
End Try
My python script looks like this:
import os
import arcpy
import sys
import glob
arcpy.KMLToLayer_conversion(sys.argv[1],sys.argv[2],sys.argv[3])
print

The path returned contains spaces? It seems so from your initial directory.
In that case the command arguments passed to the script could be wrong.
Try to enclose everything in double quotes and avoid direct manipulation of paths.
Use Path.GetDirectoryName() instead
Dim args As String
args = """" + kmlFile + """ "
args = args & """" & Path.GetDirectoryName(kmlFile) & """ test"

Replace "\" to "\\\"
Does it work?

Userfriendly way of handling config files in python?

I want to write a program that sends an e-mail to one or more specified recipients when a certain event occurs. For this I need the user to write the parameters for the mail server into a config. Possible values are for example: serveradress, ports, ssl(true/false) and a list of desired recipients.
Whats the user-friendliest/best-practice way to do this?
I could of course use a python file with the correct parameters and the user has to fill it out, but I wouldn't consider this user friendly. I also read about the 'config' module in python, but it seems to me that it's made for creating config files on its own, and not to have users fill the files out themselves.

Are you saying that the fact that the config file would need to be valid Python makes it unfriendly? It seems like having lines in a file like:
server = 'mail.domain.com'
port = 25
...etc would be intuitive enough while still being valid Python. If you don't want the user to have to know that they have to quote strings, though, you might go the YAML route. I use YAML pretty much exclusively for config files and find it very intuitive, and it would also be intuitive for an end user I think (though it requires a third-party module - PyYAML):
server: mail.domain.com
port: 25
Having pyyaml load it is simple:
>>> import yaml
>>> yaml.load("""a: 1
... b: foo
... """)
{'a': 1, 'b': 'foo'}
With a file it's easy too.
>>> with open('myconfig.yaml', 'r') as cfile:
... config = yaml.load(cfile)
...
config now contains all of the parameters.

I doesn't matter technically proficient your users are; you can count on them to screw up editing a text file. (They'll save it in the wrong place. They'll use MS Word to edit a text file. They'll make typos.) I suggest making a gui that validates the input and creates the configuration file in the correct format and location. A simple gui created in Tkinter would probably fit your needs.

I've been using ConfigParser. It's designed to read .ini style files that have:
[section]
option = value
It's quite easy to use and the documentation is pretty easy to read. Basically you just load the whole file into a ConfigParser object:
import ConfigParser
config = ConfigParser.ConfigParser()
config.read('configfile.txt')
Then you can make sure the users haven't messed anything up by checking the options. I do so with a list:
OPTIONS =
['section,option,defaultvalue',
.
.
.
]
for opt in OPTIONS:
section,option,defaultval = opt.split(',')
if not config.has_option(section,option):
print "Missing option %s in section %s" % (option,section)
Getting the values out is easy too.
val = config.get('section','option')
And I also wrote a function that creates a sample config file using that OPTIONS list.
new_config = ConfigParser.ConfigParser()
for opt in OPTIONS:
section,option,defaultval = opt.split(',')
if not new_config.has_section(section):
new_config.add_section(section)
new_config.set(section, option, defaultval)
with open("sample_configfile.txt", 'wb') as newconfigfile:
new_config.write(newconfigfile)
print "Generated file: sample_configfile.txt"

What are the drawbacks of such a solution:
ch = 'serveradress = %s\nport = %s\nssl = %s'
a = raw_input("Enter the server's address : ")
b = 'a'
bla = "\nEnter the port : "
while not all(x.isdigit() for x in b):
b = raw_input(bla)
bla = "Take care: you must enter digits exclusively\n"\
+" Re-enter the port (digits only) : "
c = ''
bla = "\nChoose the ssl option (t or f) : "
while c not in ('t','f'):
c = raw_input(bla)
bla = "Take care: you must type f or t exclusively\n"\
+" Re-choose the ssl option : "
with open('configfile.txt','w') as f:
f.write(ch % (a,b,c))
.
PS
I've read in the jonesy's post that the value in a config file may have to be quoted. If so, and you want the user not to have to write him/her-self the quotes, you simply add
a = a.join('""')
b = b.join('""')
c = c.join('""')
.
EDIT
ch = 'serveradress = %s\nport = %s\nssl = %s'
d = {0:('',
"Enter the server's address : "),
1:("Take care: you must enter digits exclusively",
"Enter the port : "),
2:("Take care: you must type f or t exclusively",
"Choose the ssl option (t or f) : ") }
def func(i,x):
if x is None:
return False
if i==0:
return True
elif i==1:
try:
ess = int(x)
return True
except:
return False
elif i==2:
if x in ('t','f'):
return True
else:
return False
li = len(d)*[None]
L = range(len(d))
while True:
for n in sorted(L):
bla = d[n][1]
val = None
while not func(n,val):
val = raw_input(bla)
bla = '\n '.join(d[n])
li[n] = val.join('""')
decision = ''
disp = "\n====== If you choose to process, =============="\
+"\n the content of the file will be :\n\n" \
+ ch % tuple(li) \
+ "\n==============================================="\
+ "\n\nDo you want to process (type y) or to correct (type c) : "
while decision not in ('y','c'):
decision = raw_input(disp)
disp = "Do you want to process (type y) or to correct (type c) ? : "
if decision=='y':
break
else:
diag = False
while not diag:
vi = '\nWhat lines do you want to correct ?\n'\
+'\n'.join(str(j)+' - '+line for j,line in enumerate((ch % tuple(li)).splitlines()))\
+'\nType numbers of lines belonging to range(0,'+str(len(d))+') separated by spaces) :\n'
to_modify = raw_input(vi)
try:
diag = all(int(entry) in xrange(len(d)) for entry in to_modify.split())
L = [int(entry) for entry in to_modify.split()]
except:
diag = False
with open('configfile.txt','w') as f:
f.write(ch % tuple(li))
print '-*- Recording of the config file : done -*-'