I am using the Linux command pdftotext -layout *.pdf to extract text from some pdf files, for data mining. The resultant text files all reside in a single folder, but they need some pre-processing before they can be used.
Issues
Issue 1: The first value of each row in each file that I am trying to access is a barcode, which can be either a 13-digit GTIN code, or a 5-digit PLU code. The problem here is that the GTIN codes are delineated with a single space character, which is hard to replace with a script, as each row also contains a description field which, naturally, also contains single spaces between words. Here I will need to replace a set of 13 numerals plus a space with the same 13 numerals plus two spaces (at least), so that a later stage of the pre-processing can replace all multiple spaces with a tab character.
Issue 2: Another problem I am facing with this pre-processing is the newlines. There are many blank lines between data rows. Some are single blank lines between the data rows, and some are two or more lines. I want to end up with no blank lines between the data rows, but each row will be delineated by a newline character.
Issue 3: The final resulting files each need to be tab separated value files, for importing into a spreadsheet. Some of the descriptions in the data rows may contain commas, so I am using TSV rather than CSV files. I only need a single tab between each value in the row.
Sample rows
(I have replaced spaces with • and newlines with ¶ characters here for clarity.)
9415077026340•Pams•Sour•Cream•&•Chives•Rice•Crackers•100g•••$1.19¶
¶
¶
9415077026296•Pams•BBQ•Chicken•Rice•Crackers•100g•••$1.19¶
¶
61424••••••••••••Yoghurt•Raisins•kg•••$23.90/kg¶
¶
9415077036349•Pams•Sliced•Peaches•In•Juice•410g•••$1.29¶
Intended result
(I have also replaced tabs with ⇥ characters here for clarity.)
9415077026340⇥Pams•Sour•Cream•&•Chives•Rice•Crackers•100g⇥$1.19¶
9415077026296⇥Pams•BBQ•Chicken•Rice•Crackers•100g⇥$1.19¶
61424⇥Yoghurt•Raisins•kg⇥$23.90/kg¶
9415077036349⇥Pams•Sliced•Peaches•In•Juice•410g⇥$1.29¶
What have I tried?
I am slowly learning more about the various Linux script utilities such as sed / grep / awk / tr, etc. There are many solutions posted in StackOverflow which resolve some of the issues that I am facing, but they are disparate and confusing when I attempt to string them all together in the way that I need them. Some are "close, but not quite" solutions, such as replacing all double newlines with a single newline between each data row. I don't need the extra row between them. I have been looking and trying several different options that are close to what I need. It would be helpful if someone could propose a solution which uses a single utility, such as sed, to solve all of the issues at once.
I have a massive (400Mb) CSV file that I need to upload into a database.
The problem is that some lines contain 16 commas (",") and some 17.
I need to find the lines that contain 17 commas so that I can fix them (shouldn't be that many).
Is there a way to search in sublime so that each line becomes visible, that repeatedly contains the same particular character?
This is a job for regular expressions!
Instructions on activating regexes in Sublime Text
You want the regex (.*,){17} - i.e., seventeen instances of any old nonsense followed by a comma.
I'm currently strugling to clean csv files generated automatically with fields containing the csv separator and the field delimiter using sed or awk or via a script.
The source software has no settings to play with to improve the situation.
Format of the csv:
"111111";"text";"";"text with ; and " sometimes "; or ;" multiple times";"user";
Fortunately, the csv is "well" formatted, the exporting software just doesn't escape or replace "forbidden" chars from the fields.
In the last few days I tried to improve my knowledge of regular expression and find expression to clean the files but I failed.
What I managed to do so far:
RegEx to find the fields (I wanted to find the fields and perform a replace inside but I didn't find a way to do it)
(?:";"|^")(.*?)(?=";"|";\n)
RegEx that find semicolon, does not work if the semicolon is the last char of the field only find one per field.
(?:^"|";")(?:.*?)(;)(?:[^"\n].*?)(?=";"|";\n)
RegEx to find the double quotes, seems to pick the first double quote of the line in online regex testers
(?:^"|";")(?:.*?)[^;](")(?:[^;].*?)(?=";"|";\n)
I thought of adding space between each chars in the fields then searching for lonely semi colon and double quotes and remove single space after that but I don't know if it's even possible and seems like a poor solution anyway.
Any standard library should be able to handle it if there is no explicit error in the CSV itself. This is why we have quote-characters and escape characters.
When you create a CSV by yourself - you may forgot handling such cases and let your final output file use this situation. AWK is not a CSV reader but simply a text processing utility.
This is what your row should rather look like.
"111111";"text";"";"text with \; and \" sometimes \"; or ;\" multiple times";"user";
So if you can still re-fetch the data, find a way to export the CSV either through the database's own functionality of csv library for the languages you work with.
In python, this would look like this:-
mywriter = csv.writer(csvfile, delimiter=';', quotechar='"', escapechar="\\")
But if you can't create csv again, the only hope is that you expect some pattern within the fields, as in this question:- parse a csv file that contains commans in the fields with awk
But this is rarely true in textual data - esp comments or posts on a webpage. Another idea in such situations would be to use '\t' as separator.
Does the newline sequence or even all escape sequences in a file count as only one character, even though it's written \n?
After I separated a one-line-file into multiple lines, only one character per line was added according to the wc -m output of the terminal.
\n is a way of representing a newline character in various languages and programs but as the name suggests, a newline is only stored in a file as a single character.
The backslash helps both computers and humans to realise you are referring to a newline character without you having to actually type one, which would be confusing in a lot of instances.
The \n notation is usually used for a single character. Use a hexdump to see the actual bytes, for example xxd.
For coding reasons which would horrify you (I'm too embarrassed to say), I need to store a number of text items in a single string.
I will delimit them using a character.
Which character is best to use for this, i.e. which character is the least likely to appear in the text? Must be printable and probably less than 128 in ASCII to avoid locale issues.
I would choose "Unit Separator" ASCII code "US": ASCII 31 (0x1F)
In the old, old days, most things were done serially, without random access. This meant that a few control codes were embedded into ASCII.
ASCII 28 (0x1C) File Separator - Used to indicate separation between files on a data input stream.
ASCII 29 (0x1D) Group Separator - Used to indicate separation between tables on a data input stream (called groups back then).
ASCII 30 (0x1E) Record Separator - Used to indicate separation between records within a table (within a group). These roughly map to a tuple in modern nomenclature.
ASCII 31 (0x1F) Unit Separator - Used to indicate separation between units within a record. The roughly map to fields in modern nomenclature.
Unit Separator is in ASCII, and there is Unicode support for displaying it (typically a "us" in the same glyph) but many fonts don't display it.
If you must display it, I would recommend displaying it in-application, after it was parsed into fields.
Assuming for some embarrassing reason you can't use CSV I'd say go with the data. Take some sample data, and do a simple character count for each value 0-127. Choose one of the ones which doesn't occur. If there is too much choice get a bigger data set. It won't take much time to write, and you'll get the answer best for you.
The answer will be different for different problem domains, so | (pipe) is common in shell scripts, ^ is common in math formulae, and the same is probably true for most other characters.
I personally think I'd go for | (pipe) if given a choice but going with real data is safest.
And whatever you do, make sure you've worked out an escaping scheme!
When using different languages, this symbol: ¬
proved to be the best. However I'm still testing.
Probably | or ^ or ~ you could also combine two characters
You said "printable", but that can include characters such as a tab (0x09) or form feed (0x0c). I almost always choose tabs rather than commas for delimited files, since commas can sometimes appear in text.
(Interestingly enough the ascii table has characters GS (0x1D), RS (0x1E), and US (0x1F) for group, record, and unit separators, whatever those are/were.)
If by "printable" you mean a character that a user could recognize and easily type in, I would go for the pipe | symbol first, with a few other weird characters (# or ~ or ^ or \, or backtick which I can't seem to enter here) as a possibility. These characters +=!$%&*()-'":;<>,.?/ seem like they would be more likely to occur in user input. As for underscore _ and hash # and the brackets {}[] I don't know.
How about you use a CSV style format? Characters can be escaped in a standard CSV format, and there's already a lot of parsers already written.
Can you use a pipe symbol? That's usually the next most common delimiter after comma or tab delimited strings. It's unlikely most text would contain a pipe, and ord('|') returns 124 for me, so that seems to fit your requirements.
For fast escaping I use stuff like this:
say you want to concatinate str1, str2 and str3
what I do is:
delimitedStr=str1.Replace("#","#a").Replace("|","#p")+"|"+str2.Replace("#","#a").Replace("|","#p")+"|"+str3.Replace("#","#a").Replace("|","#p");
then to retrieve original use:
splitStr=delimitedStr.Split("|".ToCharArray());
str1=splitStr[0].Replace("#p","|").Replace("#a","#");
str2=splitStr[1].Replace("#p","|").Replace("#a","#");
str3=splitStr[2].Replace("#p","|").Replace("#a","#");
note: the order of the replace is important
its unbreakable and easy to implement
Pipe for the win! |
We use ascii 0x7f which is pseudo-printable and hardly ever comes up in regular usage.
Well it's going to depend on the nature of your text to some extent but a vertical bar 0x7C doesn't crop up in text very often.
I don't think I've ever seen an ampersand followed by a comma in natural text, but you can check the file first to see if it contains the delimiter, and if so, use an alternative. If you want to always be able to know that the delimiter you use will not cause a conflict, then do a loop checking the file for the delimiter you want, and if it exists, then double the string until the file no longer has a match. It doesn't matter if there are similar strings because your program will only look for exact delimiter matches.
This can be good or bad (usually bad) depending on the situation and language, but keep mind mind that you can always Base64 encode the whole thing. You then don't have to worry about escaping and unescaping various patterns on each side, and you can simply seperate and split strings based on a character which isn't used in your Base64 charset.
I have had to resort to this solution when faced with putting XML documents into XML properties/nodes. Properties can't have CDATA blocks in them at all, and nodes escaped as CDATA obviously cannot have further CDATA blocks inside that without breaking the structure.
CSV is probably a better idea for most situations, though.
Both pipe and caret are the obvious choices. I would note that if users are expected to type the entire response, caret is easier to find on any keyboard than is pipe.
I've used double pipe and double caret before. The idea of a non printable char works if your not hand creating or modifying the file. For quick random access file storage and retrieval field width is used. You don't even have to read the file.. your literally pulling from the file by reference. This is how databases do some storage.. but they also manage the spaces between records and such. And it introduced the problem of max data element width. (Index attach a header which is used to define the width of each element and it's data type in the original old days.. later they introduced compression with remapping chars. This allows for a text file to get about 1/8 the size in transmission.. variable length char encoding for the win
make it dynamic : )
announce your control characters in the file header
for example
delimiter: ~
escape: \
wrapline: $
width: 19
hello world~this i$
s \\just\\ a sampl$
e text~$someVar$~h$
ere is some \~\~ma$
rkdown strikethrou$
gh\~\~ text
would give the strings
hello world
this is \just\ a sample text
$someVar$
here is some ~~markdown strikethrough~~ text
i have implemented something similar:
a plaintar text container format,
to escape and wrap utf16 text in ascii,
as an alternative to mime multipart messages.
see https://github.com/milahu/live-diff-html-editor