Sure a very simple question but I can't seem to find the terminology to find the answer in a search!
I'm using a file-uploader CGI script. Inside the CGI script is some code that generates some HTML. In the HTML I need to put an email address using the # symbol, however this breaks the script. What is the correct way to escape the # symbol in a CGI script?
The error when using the # symbol is:
"FileChucker: load_external_prefs(): Error processing your prefs file ('filechucker_prefs.cgi'): Global symbol "#email" requires explicit package name at (eval 16) line 1526."
Many thanks for any help
Update..
Hi All, many thanks for the replies - I guess it is perl.. (shows my ignorance of what's going on here perfectly!). The code below shows the problem the # in 'email#domain.com'.
'test$PREF{app_output_template} = qq`
%%%ifelse-onpage_uploader%%%
<div id="fcintro">If you're using a mobile or tablet and have problems uploading, we recommend emailing your CV to: email#domain.com<br><span class"upload_limits">We can accept Adobe PDF, Microsoft Word and all popular image and text file types. (max total upload size: 7MB)</span></div>
%%%else%%%
%%subtitle%%
%%%endelse-onpage_uploader%%%
%%app_output_body%%'
Try # instead of #.
Reference: http://www.w3schools.com/tags/ref_ascii.asp
Related
I just sat down to write my first Nim script to parse a .vcf (Variant Call Format) file. This file format stores genetic mutations from sequencing data.
For scripting languages, I 'grew up' on Perl and later migrated to Python, but I would love to use a language with the speed that Nim offers. I realize Nim is still young, but I couldn't even find a clear example for how to open and read a .gz (gzip) file (preferably line by line).
Can anyone provide a simple example to open and read a gzip file using Nim, line by line?
In Python, I'm accustomed to the following (uber-simple) code:
import gzip
my_file = gzip.open('my_file.vcf.gz', 'w')
for line in my_file:
# do something
my_file.close()
I have seen related questions, but they're not clear. The posts are also relatively old and I hope/suspect something better has come about. Here's what I've found:
Read gzip-compressed file line by line
File, FileStream, and GZFileStream
Reading files from tar.gz archive in Nim
Really appreciate it.
P.S. I also think it would be useful if someone created a Nim tag in StackOverflow. I do not have the reputation to create tags.
Just in case you need to handle VCF rather than .gz, there's a nice wrapper for htslib written by Brent Pedersen:
https://github.com/brentp/hts-nim
You need to install the htslib in your system, and then require the library in your .nimble file with requires "hts", or install the library with nimble install hts. If you are going to do NGS analysis in Nim you'll need it.
The code you need:
import hts
var v:VCF
doAssert open(v, "myfile.vcf.gz")
# Here you have the VCF file loaded in v, and can access the headers through
# v.header property
for record in v:
# Here you get a Record object per line, e.g. extract the Ref and Alts:
echo v.REF, " ", v.ALT
v.close()
Be sure to follow the docs, because some things differ from python, specially when getting the INFO and FORMAT fields.
Checkout the whole Brent repo. It has plenty of wrappers, code samples and utilities to handle NGS problems (e.g. an ultrafast coverage tool utility called Mosdepth).
Per suggestion from Maurice Meyer, I looked at the tests for the Nim zip package. It turned out to be quite simple. This is my first Nim script, so my apologies if I didn't follow convention, etc.
import zip/gzipfiles # Import zip package
block:
let vcf = newGzFileStream("my_file.vcf.gz") # Open gzip file
defer: outFile.close() # Close file (like a 'final' statement in 'try' block)
var line: string # Declare line variable
# Loop over each line in the file
while not vcf.atEnd():
line = vcf.readLine()
# Cure disease with my VCF file
To install the zip package, I simply ran because it is already in the Nim package library:
> nimble refresh
> nimble install zip
I tried to use Nim some time ago to parse a fastq or fastq.gz file.
The code should be available here:
https://gitlab.pasteur.fr/bli/qaf_demux/blob/master/Nim/src/qaf_demux.nim
I don't remember exactly how this works, but apparently, I did an import zip/gzipfiles and used newGZFileStream on the input file name to obtain a Stream from which lines can be read using .readLine() in this piece of code:
proc fastqParser(stream: Stream): iterator(): Fastq =
result = iterator(): Fastq =
var
nameLine: string
nucLine: string
quaLine: string
while not stream.atEnd():
nameLine = stream.readLine()
nucLine = stream.readLine()
discard stream.readLine()
quaLine = stream.readLine()
yield [nameLine, nucLine, quaLine]
It is used in something that amounts to this piece of code:
let inputFqs = fastqParser(newGZFileStream($inFastqFilename))
Hopefully you can adapt this to your case.
My .nimble file has a requires "zip#head". I suppose this triggers the installation of zip/gzipfiles.
Using VBA, I am trying to download images from url, renaming them and saving them to folder.
I have found code that facilitates this, but it seems that all "names" with a "/" in it won't download.
Is this possible? Is there a way around it?
I have tried the code from the link Downloading Images from URL and Renaming
No error messages are provided. The images simply won't download.
Files are not allowed to have a / in their name, that's always been the case. The code works unless you put a symbol that's not allowed, which are / \ : * ? " < > |
I have a latex file which needed to include snippets of Lua code (for display, not execution), so I used the minted package. It requires latex to be run with the latex -shell-escape flag.
I am trying to upload a PDF submission to arXiv. The site requires these to be submitted as .tex, .sty and .bbl, which they will automatically compile to PDF from latex. When I tried to submit to arXiv, I learned that there was no way for them to activate the -shell-escape flag.
So I was wondering if any of you knew a way to highlight Lua code in latex without the -shell-escape flag. I tried the listings package, but I can't get it to work for Lua on my Ubuntu computer.
You can set whichever style you want inline using listings. It's predefined Lua language has all the keywords and associated styles identified, so you can just change it to suit your needs:
\documentclass{article}
\usepackage{listings,xcolor}
\lstdefinestyle{lua}{
language=[5.1]Lua,
basicstyle=\ttfamily,
keywordstyle=\color{magenta},
stringstyle=\color{blue},
commentstyle=\color{black!50}
}
\begin{document}
\begin{lstlisting}[style=lua]
-- defines a factorial function
function fact (n)
if n == 0 then
return 1
else
return n * fact(n-1)
end
end
print("enter a number:")
a = io.read("*number") -- read a number
print(fact(a))
\end{lstlisting}
\end{document}
Okay so lhf found a good solution by suggesting the GNU source-hightlight package. I basically took out each snippet of lua code from the latex file, put it into an appropriately named [snippet].lua file and ran the following on it to generate a [snippet]-lua.tex :
source-highlight -s lua -f latex -i [snippet].lua -o [snippet]-lua.tex
And then I included each such file into the main latex file using :
\input{[snippet]-lua}
The result really isn't as nice as that of the minted package, but I am tired of trying to convince the arXiv admin to support minted...
I just downloaded psychopy this morning and have spent the day trying to figure out how to work with builder view. I watched the youtube video "Build your first PsychoPy experiment (Stroop task)" by Jon Pierce. In his video he was explaining how to make a conditions file with excel that would be used in his experiment. I wanted to make a very similar test where images would appear and subjects would be required to give a yes or no answer to them (the correct answer is already predefined). In his conditions file he had the columns 'word' 'colour' and 'corrANS'. I was wondering if instead of a 'word' column, I can have an 'image' column. In this column I would like to upload all my images to them in the same way I would words, and have them correlated to a correct answer of either 'yes' or 'no'. We tried doing this and uploaded images to the conditions file, but we haven't had any success in running the test successfully and were hoping somebody could help us.
Thank you in advance.
P.S. we are not familiar with python, or code in general, so we were hoping to get this running using the builder view.
EDIT: Here is the error message we are receiving when running the program
#### Running: C:\Users\mr00004\Desktop\New folder\1_lastrun.py
4.8397 ERROR Couldn't find image file 'C:/Users/mr00004/Desktop/New folder/PPT Retention 1/ Slide102.JPG'; check path?
Traceback (most recent call last):
File "C:\Users\mr00004\Desktop\New folder\1_lastrun.py", line 174, in
image.setImage(images)
File "C:\Program Files (x86)\PsychoPy2\lib\site-packages\psychopy-1.80.03-py2.7.egg\psychopy\visual\image.py", line 271, in setImage
maskParams=self.maskParams, forcePOW2=False)
File "C:\Program Files (x86)\PsychoPy2\lib\site-packages\psychopy-1.80.03-py2.7.egg\psychopy\visual\basevisual.py", line 652, in createTexture
% (tex, os.path.abspath(tex))#ensure we quit
OSError: Couldn't find image file 'C:/Users/mr00004/Desktop/New folder/PPT Retention 1/ Slide102.JPG'; check path? (tried: C:\Users\mr00004\Desktop\New folder\PPT Retention 1\ Slide102.JPG)
Yes, certainly, that is exactly how PsychoPy is designed to work. Simply place the image names in a column in your conditions file. You can then use the name of that column in the Builder Image component's "Image" field. The appropriate image file for a given trial will be selected.
It is difficult to help you further, though, as you haven't specified what went wrong. "we haven't had any success" doesn't give us much to go on.
Common problems:
(1) Make sure you use full filenames, including extensions (.jpg, .png, etc). These aren't always visible in Windows at least I think, but they are needed by Python.
(2) Have the images in the right place. If you just use a bare filename (e.g. image01.jpg), then PsychoPy will expect that the file is in the same directory as your Builder .psyexp file. If you want to tidy the images away, you could put them in a subfolder. If so, you need to specify a relative path along with the filename (e.g. images/image01.jpg).
(3) Avoid full paths (starting at the root level of your disk): they are prone to errors, and stop the experiment being portable to different locations or computers.
(4) Regardless of platform, use forward slashes (/) not backslashes (\) in your paths.
make a new folder in H drive and fill in the column of image in psychopy as e.g. 'H:\psych\cat.jpg' it works for me
I have a git repo project in eclipse which I have been documenting using doxygen (v1.8.4).
If I run the latex make ion a fresh clone of the project it runs fine and the PDF is made.
However, if I then run a doxy build, which completes OK, then attempt to run the latex make, it fails for
! Package inputenc Error: Keyboard character used is undefined
(inputenc) in inputencoding `utf8'.
See the inputenc package documentation for explanation.
Type H <return> for immediate help.
...
I have tried switching the encoding of the doxyfile by setting DOXYFILE_ENCODING to ISO-8859-1 with no change in the result... How can I fix this?? Thanks.
EDIT: I have used no non-UTF-8 chars as far as I know in my files, the file referenced before the error is very short and definitely doesn't have non-UTF-8 chars in it. I've even tried clearing my latex output dir and building from scratch with no luck...
EDIT: Irealised that the doxy build only appears to run correctly. It doesnt show any errors, but it should, for example run DOT and build about 10 graphs. The console output says Running dot, but it doesn't say generating graph (n/x) like it should when it actually makes the graphs...
Short answer: So by a slow process of elimination I found that this was caused by a single apostrophe in a file that had appeared to be already built and made without error!!
Long answer: Firstly I used used the project properties to flip the encoding from the default Cp1252 to UTF-8. Then I started removing files one-by-one until rebuilding and remaking after each removal, until the make ran successfully. I re-added all files, but deleted the content in the most recently removed file and tested the make - to confirm it was this file and only this file that caused the issue. the make ran fine. So I pasted the content back into the empty file, and started deleting smaller and smaller sections of the file, again rebuilding and remaking each time until I was left with a good make without the apostrophe and a bad one with it... I simply retyped the apostrophe (as this would then force it to be a UTF-8 char) and success!! Such an annoying bug!
Dude you made it a hard way. Why not use python to do the work for you:
f = open(fn,"rb")
data = f.read()
f.close()
for i in range(len(data)):
ch = data[i]
if(ch > 0x7F): # non ASCII character
print("char: %c, idx: %d, file: %s"%(ch,i,fn))
str2 = str(data[i-30:i+30])#.decode("utf-8")
print("txt: %s" % (str2))