When I have $$\mathbf{x}$$ in my .Rmd file, and use exams2moodle with the pandoc-mathml converter, the xml file contains an "𝐱" character, which needs to be replaced with an "x" character before moodle will import the quiz question (because moodle will give an error saying the file is not UTF-8 without BOM.)
I wonder what are the most practical workarounds? Is this a bug? Thanks!
Minimal example: Here is minimal_example.Rmd
Question
========
Stare hard at the variable.
$$\mathbf{x}$$
What is its value?
Solution
========
If you think hard enough, you will know it is 12.
Meta-information
================
extype: num
exsolution: 12
exname: minimal_example
extol: 0
Here is the minimal_example.r
library("exams")
exams2moodle("minimal_example.Rmd", converter="pandoc-mathml")
And... here is a snippet of the resulting .xml file.
...
<questiontext format="html">
<text><![CDATA[<p>
<p>Stare hard at the variable. <math display="block" xmlns="http://www.w3.org/1998/Math/MathML"><semantics><mstyle mathvariant="bold"><mi>𝐱</mi></mstyle><annotation encoding="application/x-tex">\mathbf{x}</annotation></semantics></math> What is its value?</p>
</p>]]></text>
</questiontext>
...
If I try importing the XML to my school's moodle, I get a dmlwriteexeption error. If I replace the "𝐱" with "x" the XML imports fine.
I am fairly certain my moodlequiz.xml file does not contain a BOM.
$ file moodlequiz.xml
moodlequiz.xml: XML 1.0 document, UTF-8 Unicode text, with very long lines
$ hexdump -n 3 -C moodlequiz.xml
00000000 3c 3f 78 |<?x|
00000003
I consider this question resolved. Hopefully nobody else has this issue, and I will use one of the proposed workarounds for my own files. Thanks!
TL;DR
exams2moodle(..., converter = "pandoc-mathml") seems to work correctly and produces an UTF-8 encoded XML file moodlequiz.xml. The problem on your end appears to be caused by a BOM (byte order mark) in your XML file. It is unclear to me whether this is introduced through exams2moodle() or through an editor on your end.
Either you can remove the BOM manually or you can avoid the UTF-8 encoding altogether by using exams2moodle(..., converter = "pandoc-mathml-ascii"). The latter requires at least version 2.4-0 of the package.
Replication
Thanks for providing a reproducible example. I ran your example code - both on a Linux machine running in an UTF-8 locale and a Windows 10 machine - and can confirm that I get exactly the same XML code containing the UTF-8 encoded bold x: 𝐱. However, I have no problem importing that into my Moodle system.
Possible sources of the problem
So I looked up what the Moodle error message is about. Moodle does not accept UTF-8-encoded files with a BOM (byte order mark) at the beginning. Some systems use a BOM at the beginning of a file to declare how the file is encoded. See:
Moodle documentation: https://docs.moodle.org/39/en/UTF-8_and_BOM
Wikipedia with general information: https://en.wikipedia.org/wiki/Byte_order_mark
The moodlequiz.xml I produced on the two systems I mentioned above have no BOM. So I suspect that either your R setup produces a file with a BOM or the BOM is inserted later, e.g., after opening the XML file with an editor. The Moodle documentation above has some information on what you can do to detect the BOM and get rid of it. Hopefully, this lets you debug the problem on your end. If the BOM was produced by exams2moodle() (as opposed to your editor for example) and you find out how to avoid that, please let me know.
Alternative solution
In principle it is possible to replace the UTF-8 encocded characters by the corresponding HTML entities. For example, in this particular case we have a "MATHEMATICAL BOLD SMALL X" with Unicode U+1D431 (see https://www.w3.org/Math/characters/bold.html). Thus, we can also represent it as 𝐱 (hexadecimal) or 𝐱 (decimal). Then the XML file can be in ASCII while still leading to the same output in HTML.
While pandoc is generally designed to work with UTF-8 throughout it also has support for (hexa)decimal escapes in certain conversions, see https://pandoc.org/MANUAL.html#option--ascii. And luckily it is possible to combine the --mathml with the --ascii option. There was only a small bug in how R/exams passed on the option to the rmarkdown::pandoc_convert() function which I just fixed. So you need at least version 2.4-0 of exams and can then do:
exams2moodle(..., converter = "pandoc-mathml-ascii")
which yields a moodlequiz.xml in ASCII instead of UTF-8.
Related
In 2001 German scene group Farbrausch released a demo called "fuenf" (in your face). pouet.net It contains a 5 Byte executable which could be rather considered a troll approach than a demo. If you run it your hear a weird sound and it could crash your computer. At least it produces a sound. Whatever.
The hexadecimal content is:
95cd 21eb fc
And the binary representation is:
10010101 11001101 00100001 11101011 11111100
Using xxd I also get the printable chars from the content, which are:
..!..
And that makes me a little confused. Looking up the values in the ASCII table (e.g. here), I get this as a result:
•Í!ëü
At least the exclamation mark is correct.
But how does 95cd21ebfc translate into ..!..?
Side note:
file -bi fuenf.com sais the encoding is not known:
charset=unknown-8bit
And iconv -f ISO-8859-1 -t UTF-8 fuenf.com returns
Í!ëü
Which leads to the assumption, that XXD simply cannot decode the content and therefore just uses default results, like the dot?
First of all, this is not a text file, so looking at it as one makes no sense. It's instructions.
Secondly, even if it could be interpreted as text, you would need to know the encoding. It's definitely not ASCII, because that only defines symbols in the range 0-127 (and the 3rd byte here is the only one in that range, which maps to '!'). The "extended ASCII" table you link to is only one of many possible code pages that give meaning to the value from 128-255, but there are many of those code pages. Calling it "extended ASCII" is misleading, because it suggests that ASCII created an updated standard for this, which they did not. For a while, computer vendors just did whatever they wanted with those additional characters, and some of them became quasi-standards by virtue of being included in DOS, Windows, etc. Or they got standardized by ISO (you tried iso-8859-1, which is one such standard).
I'm trying to read a file line-by-line in Ada, it's a XML text file. I'm following the instructions here:
http://rosettacode.org/wiki/Read_a_file_line_by_line#Ada
However there's a problem that annoys me: the "Get_Line" function seems to be unaware of byte-order marks and reads them as part of the text itself, which means that when I raed the lines, the first one will always start with some extra bytes that should not be there.
While removing the extra bytes manually from the string is no big deal it seems strange to me that a function dedicated to text input/output is unaware of BOMs, there must be a way to read a text file in ada without having to worry about this... is there?
Ada.Text_IO is specified to handle ISO-8859-1 encoded text, so ignoring an UTF-8 feature is the proper thing to do.
If Ada.Wide_Text_IO and Ada.Wide_Wide_Text_IO also output the byte-order-mark, when asked to read UTF-8 encoded text, then you should consider reporting it as a bug to GCC - but as there is quite a lot of implementation defined details for the text I/O packages in Ada, you should be ready for a "wont fix" answer.
One possibility is using the stream attributes and making a UTF_8 file-type to handle the BOM reading-and-discarding.
I was trying to find a solution for my problem and after looking at the forums I couldn't so I'll explain my problem here.
We receive a csv file from a client with some special characters and encoded as unknown-8bit. We convert this csv file to xml using an awk script. With the xml file we make an API call to our system using utf-8 as default encoding. The response is an error with following information:
org.apache.xerces.impl.io.MalformedByteSequenceException: Invalid byte 1 of 1-byte UTF-8 sequence
The content of the file is as bellow:
151215901579-109617744500,sandra,sandra,Coesfeld,,Coesfeld,48653,DE,1,2.30,ASTRA 16V CAVALIER CALIBRA TURBO BLUE 10,53.82,GB,,.80,3,ASTRA 16V CAVALIER CALIBRA TURBO BLUE 10MM 4CORE IGNITION HT LEADS WIRES MLR.CR,,sandra#online.de,parcel1,Invalid Request,,%004865315500320004648880276,INTL,%004865315500320004648880276,1,INTL,DPD,180380,INTL,2.30,Send A2B Ltd,4th Floor,200 Gray’s Inn Road,LONDON,,WC1X8XZ,GBR,
I think the problem is in the field "200 Gray’s Inn Road" cause when I use utf-8 encoding it automatically converts "'" character by a x92 value.
Does anybody know how can I handle this?
Thanks in advance,
Sandra
Find out the actual encoding first, best would be asking the sender.
If you cannot do so, and also for sanity-checking, the unix command file is very useful for that (the linked page shows more options).
Next step, convert to UTF-8.
As it is obviously an ASCII-based encoding, you could just discard all non-ASCII or replace them on encoding, if that loss is acceptable.
As an alternative, open it in the editor of your choice and flip the encoding used for interpreting the data until you get something useful. My guess is you'll have either Latin-1 or Windows-1252, but check it for yourself.
Last step, do what you wanted to do, in comforting knowledge that you now have valid UTF-8.
Obviously, don't pretend it's UTF-8 if it isn't. Find out what the encoding is, or replace all non-ASCII characters with the UTF-8 REPLACEMENT CHARACTER sequence 0xEF 0xBF 0xBD.
Since you are able to view this particular sample just fine, you apparently already know which encoding it is (even if you don't know that you know -- it would be whatever your current set-up is using) -- I would guess Windows-1252 which uses 0x92 for a curvy right single quote.
Is there a native method in R to test if a file on disk is an ASCII text file, or a binary file? Similar to the file command in Linux, but a method that will work cross platform?
The file.info() function can distinguish a file from a dir, but it doesn't seem to go beyond that.
If all you care about is whether the file is ASCII or binary...
Well, first up definitions. All files are binary at some level:
is.binary <- function(file){
if(system.type() != "quantum computer"){
return(TRUE)
}else{
return(cat=alive&dead)
}
}
ASCII is just an encoding system for characters. It is therefore impossible to tell if a file is ASCII or binary, because ASCII-ness is a matter of interpretation. If I save a file and decide that binary number 01001101 is Q and 01001110 is Z then you might decode this as ASCII but you'll get the wrong message. Luckily the Americans muscled in and said "Hey, everyone use ASCII to code their text! You get 128 characters and a parity bit! Woo! Go USA!". IBM tried to tell people to use EBCDIC but nobody listened. Which was A Good Thing.
So everyone was packing ASCII-coded text into their 8-bit bytes, and using the eighth bit for parity checking. But then people stopped doing parity checking because TCP/IP handled all that, which was also A Good Thing, and the eighth bit was expected to be zero. If not, there was trouble.
Because people (read "Microsoft") started abusing the eighth bit, and making up their own encoding schemes, and so unless you knew what encoding scheme the file was using, you were stuffed. And the file very rarely told you what encoding scheme it was. And now we have Unicode and even more encoding schemes. And that is a third Good Thing. But I digress.
Nowadays when people ask if a file is binary, what they are normally asking is "Does any byte in this file have it's highest bit set?". Which you can do in R by reading a raw file connection as unsigned integers and testing the highest value. Something like:
is.binary <- function(filepath,max=1000){
f=file(filepath,"rb",raw=TRUE)
b=readBin(f,"int",max,size=1,signed=FALSE)
return(max(b)>128)
}
This will by default test only at most the first 1000 characters. I think the file command does something similar.
You may want to change the test to check for printable character codes, and whitespace, and line feed, carriage return, and other codes you might want to consider plausible in your non-binary files...
Well, how would you do that? I guess you can't without reading (parts or all of) the file, which is why files extensions are used to signal content type.
I looked into that years ago---and as I recall, the file(1) apps actually reads the first few header bytes of a file and compares that to what is stored in a lookup table. Sounds like a good candidate for an add-on package to me..
The example section of the manual for ?raw uses this:
isASCII <- function(txt) all(charToRaw(txt) <= as.raw(127))
Sometimes when copying stuff into PostgreSQL I get errors that there's invalid byte sequences.
Is there an easy way using either vim or other utilities to detect byte sequences that cause errors such as: invalid invalid byte sequence for encoding "UTF8": 0xde70 and whatnot, and possibly and easy way to do a conversion?
Edit:
What my workflow is:
Dumped sqlite3 database (from trac)
Trying to replay it in postgresql
Perhaps there's an easier way?
More Edit:
Also tried these:
Running enca to detect encoding of the file
Told me it was ASCII
Tried iconv to convert from ASCII to UTF8. Got an error
What did work is deleting the couple erroneous lines that it complained about. But that didn't really solve the real problem.
Based on one short sentence, it sounds like you have text in one encoding (e.g. ANSI/ASCII) and you are telling PostgreSQL that it's actually in another encoding (Unicode UTF8). All the different tools you would be using: PostgreSQL, Bash, some programming language, another programming language, other data from somewhere else, the text editor, the IDE, etc., all have default encodings which may be different, and some step of the way, the proper conversions are not being done. I would check the flow of data where it crosses these kinds of boundaries, to ensure that either the encodings line up, or the encodings are properly detected and the text is properly converted.
If you know the encoding of the dump file, you can convert it to utf-8 by using recode. For example, if it is encoded in latin-1:
recode latin-1..utf-8 < dump_file > new_dump_file
If you are not sure about the encoding, you should see how sqlite was configured, or maybe try some trial-and-error.
I figured it out. It wasn't really an encoding issue.
SQLite's output escaped strings differently than Postgres expects. There were some cases where 'asdf\xd\foo' was outputted. I believe the '\x' was causing it to expect the following characters to be unicode encoding.
Solution to this is dumping each table individually in CSV mode in sqlite 3.
First
sqlite3 db/trac.db .schema | psql
Now, this does the trick for the most part to copy the data back in
for table in `sqlite3 db/trac.db .schema | grep TABLE | sed 's/.*TABLE \(.*\) (/\1/'`
do
echo ".mode csv\nselect * from $table;" | sqlite3 db/trac.db | psql -c "copy $table from stdin with csv"
done
Yeah, kind of a hack, but it works.