Copying the template file to its final destination/name does not work on Mac OS Big Sur

[kellertuer]

I am not yet sure what causes this, copying the template file and renaming it worked and brought me the pdf. I have to check what might be different here after I have found the place where the coping takes place.

[gerw]

I have no clue what you are talking about.

[kellertuer]

Calling doi2pdf now runs without an error.
It creates a template file, but not a pdf file in the folder I am in.
Copying said template file and renaming it to a pdf yields the correct pdf.
So something in the final copying does not work on Mac OS.
But I can currently not see where this is done, since shell/php/python is quite a mix and the php code is quite long with a lot of functions, none of which have documented functionality.

[gerw]

Please give some sensible information. For example, what is the output of doi2pdf?

[kellertuer]

Well, I had to check myself first, here's one that provides more information and not just output without an error

❯ doi2pdf 10.1007/978-3-319-68445-1_6
Traceback (most recent call last):
  File "/Users/ronnber/Repositories/numapde/numapde-bibliography/mathbin/doi2pdfname.py", line 9, in <module>
    tree = etree.parse(sys.argv[1], parser=parser)
  File "src/lxml/etree.pyx", line 3521, in lxml.etree.parse
  File "src/lxml/parser.pxi", line 1859, in lxml.etree._parseDocument
  File "src/lxml/parser.pxi", line 1885, in lxml.etree._parseDocumentFromURL
  File "src/lxml/parser.pxi", line 1789, in lxml.etree._parseDocFromFile
  File "src/lxml/parser.pxi", line 1177, in lxml.etree._BaseParser._parseDocFromFile
  File "src/lxml/parser.pxi", line 615, in lxml.etree._ParserContext._handleParseResultDoc
  File "src/lxml/parser.pxi", line 725, in lxml.etree._handleParseResult
  File "src/lxml/parser.pxi", line 654, in lxml.etree._raiseParseError
  File "/tmp/2368618976", line 1
lxml.etree.XMLSyntaxError: Document is empty, line 1, column 1
INFO: This is doi2pdf 2017.1!
INFO: checking for php wrappers (should be all yes):
INFO:  - openssl: yes
INFO:  - http:    yes
INFO:  - https:   yes
INFO: Fetching http://dx.doi.org/10.1007/978-3-319-68445-1_6
INFO: Fetching https://dx.doi.org/10.1007/978-3-319-68445-1_6
INFO: Fetching http://link.springer.com/10.1007/978-3-319-68445-1_6
INFO: Fetching https://link.springer.com/10.1007/978-3-319-68445-1_6
INFO: Fetching https://link.springer.com/chapter/10.1007%2F978-3-319-68445-1_6
INFO: Fetching https://idp.springer.com/authorize?response_type=cookie&client_id=springerlink&redirect_uri=http%3A%2F%2Flink.springer.com%2Fchapter%2F10.1007%252F978-3-319-68445-1_6

[gerw]

I don't think that this is the entire output.

[kellertuer]

Well, that's all that is in my terminal, what are you missing?

[kellertuer]

Invested some time and it might be curl does not work properly, so now doi2pdfname does actually work, but I am back to output without an error message (see below) that still does not do the final copy from said tmp file to the right place&name.

❯ doi2pdf 10.1007/978-3-319-68445-1_6
INFO: This is doi2pdf 2017.1!
INFO: checking for php wrappers (should be all yes):
INFO:  - openssl: yes
INFO:  - http:    yes
INFO:  - https:   yes
INFO: Fetching http://dx.doi.org/10.1007/978-3-319-68445-1_6
INFO: Fetching https://dx.doi.org/10.1007/978-3-319-68445-1_6
INFO: Fetching http://link.springer.com/10.1007/978-3-319-68445-1_6
INFO: Fetching https://link.springer.com/10.1007/978-3-319-68445-1_6
INFO: Fetching https://link.springer.com/chapter/10.1007%2F978-3-319-68445-1_6
INFO: Fetching https://idp.springer.com/authorize?response_type=cookie&client_id=springerlink&redirect_uri=http%3A%2F%2Flink.springer.com%2Fchapter%2F10.1007%252F978-3-319-68445-1_6
INFO: Fetching http://link.springer.com/chapter/10.1007%2F978-3-319-68445-1_6
INFO: Fetching https://link.springer.com/chapter/10.1007%2F978-3-319-68445-1_6
INFO: Fetching https://link.springer.com/content/pdf/10.1007%2F978-3-319-68445-1.pdf
INFO: PDF/PS found at https://link.springer.com/content/pdf/10.1007%2F978-3-319-68445-1.pdf
INFO: Writing contents to /tmp/312914748,

[gerw]

This just means that doi2pdfname failed to produce a pdf name, see https://github.com/gerw/mathbin/blob/master/doi2pdf#L65. Hence, doi2pdf just saves the pdf in a temporary file.

[kellertuer]

The -z means empty? Hm, but

❯ doi2pdfname.sh 10.1007/978-3-319-68445-1_6
Nielsen_Barbaresco_Celledoni_Eidnes_Eslitzbichler_Schmeding_Celledoni_Eidnes_Eslitzbichler_Schmeding__Geometric_Science_of_Information_BOOK.pdf

Produces a name – ok it includes both the editors (the first two) and the authors, but that's a detail; so it does produce a name.

Edit: Yes compared to above, I updated/changes curl; I might add a file here explaining how Mac OS users can use this nice script collection.

[gerw]

Are the variables $DOI and $FN in doi2pdf assigned correctly?

[kellertuer]

Yes. If I do a echo $DOI directly after its definition (ie. after line 54) and similarly a echo $FN after line 62 the beginning of the output is

❯ doi2pdf 10.1007/978-3-319-68445-1_6
10.1007/978-3-319-68445-1_6
Nielsen_Barbaresco_Celledoni_Eidnes_Eslitzbichler_Schmeding_Celledoni_Eidnes_Eslitzbichler_Schmeding__Geometric_Science_of_Information_BOOK.pdf
INFO: This is doi2pdf 2017.1!
[...]

[gerw]

And the file is still saved at the wrong place? Strange.

Is $filename correct at https://github.com/gerw/mathbin/blob/master/doi2pdf.php#L532 ??

[kellertuer]

The tmp file is created correctly but the final move/copy does not seem to happen.

The filename printed with write_info($filename); seems to be correct, yes. I will further investigate tonight.

[gerw]

There is no copying involved. The filename is passed to scan_for_pdf (https://github.com/gerw/mathbin/blob/master/doi2pdf.php#L533) and then the file is saved directly there: https://github.com/gerw/mathbin/blob/master/doi2pdf.php#L343.

Your observed behavior seems to be very strange.

[kellertuer]

It seems to have been some strange behaviour in curl or something. Installing curl via brew (again) has solved the problem. Should I maybe add a small part to the Readme how one can use this nice collection of scripts also with Mac OS?

[gerw]

Yes, feel free to set up a pull request.

[kellertuer]

I added #7 which finishes this issue.