How do I skip a file that gives an error when using fileDatastore to loop through a folder of pdfs?

I am mining text from several thousand pdfs in a folder using the Text Analytics Toolbox. I am using fileDatastore to loop through them. Some of the pdfs are encrypted, which gives an error with extractFileText. I have added a try,catch segment to skip those files, but when it catches the error it goes back to try and reads the same file again. The loop never ends. How do I increment the counter so that it will move on past the bad file? Here is part of the code:

    fds = fileDatastore('File*.pdf','ReadFcn',@extractFileText);
    while hasdata(fds)
    % extract and prepare text
    try % be prepared for error such as locked pdf
        text=read(fds); % this is where error occurs
    catch
        disp('encrypted pdf');
        continue
    end
    text=erasePunctuation(text);
    % etc. (other text-parsing)
    ...
end

Answer 1

[Allen]

I figured it out. The read statement is what moves the file pointer, and if it gives an error then the pointer stays put. I solved the problem by making the read function fileparts, obtaining the filename from that, and then using try,catch with extractFileText on that file.

[Eniola Oluwakoya]

Hi, could you share more light on how you made the read function fileparts?

Answer 2

[Allen]

fileparts is a Matlab function that parses out the parts of the file name. It is what is executed when read is executed. Here is the code that worked. info contains the filename parts. I test to see if the name is valid with try...catch.

% First make a structure to hold the files.
fds = fileDatastore('GQquads/*GQ*.pdf','ReadFcn',@fileparts);

% Loop through files

while hasdata(fds)
    % read the next entry
    [~,info]=read(fds);
    % test to see if it is a valid file (can you extract filename?)
    try
        text=extractFileText(info.Filename);
    catch
        % display name of bad file
        info.Filename
        continue
    end
 num = info.Filename;
 num = extractBetween(num,'-','.');
 num
 nums = [nums num];
 
% (text preparation)

end

[Eniola Oluwakoya]

This helped a lot, thank you