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petermr / openVirus

aggregation of scholarly publications and extracted knowledge on viruses and epidemics.
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getpapers error: "the syntax of the command is incorrect" #55

Open kareenasingh opened 4 years ago

kareenasingh commented 4 years ago

Capture

facing the above issue while using getpapers. outcome error- the syntax of the command is incorrect. kindly help out windows 10 user

Priya-Jk-15 commented 4 years ago

Screenshot (34)

Typing the syntax, Outcome - the system cannot find the file specified

What can I change in the syntax? Kindly suggest me.

Priya-Jk-15 commented 4 years ago

Screenshot (36)

Changing the syntax as above, Info- found 3255 open acess results But Warn - this version of getpapers wasn't built with this version of the EuPMC api in mind How do I get rid of it?

petermr commented 4 years ago

Well done!

Warn - this version of getpapers wasn't built with this version of the EuPMC api in mind

This is because EPMC has been updated since getpapers was written. It's a warning, not an error. If we have a Node programmer then I guess it's possible to update the API if necessary. But so far there haven't been problems. So just note in the docs that users can ignore this.

The next thing is to actually download files. The -n has stopped any downloads. To download you need to remove it and also specify an output directory. And keep -k 100 or you will fill your disk!

Have a look at TIGR2ESS to see a typical command.

kareenasingh commented 4 years ago

[image: Capture.1 PNG.PNG]

@Peter Murray-Rust pm286@cam.ac.uk from where should i get access to the above extracted files?

On Thu, May 21, 2020 at 9:07 PM petermr notifications@github.com wrote:

Well done!

Warn - this version of getpapers wasn't built with this version of the EuPMC api in mind

This is because EPMC has been updated since getpapers was written. It's a warning, not an error. If we have a Node programmer then I guess it's possibly to update the API if necessary. But so far there haven't been problems. So just note in the docs that users can ignore this.

The next thing is to actually download files. The -n has stopped any downloads. To download you need to remove it and also specify an output directory. And keep -k 100 or you will fill your disk!

Have a look at TIGR2ESS to see a typical command.

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/petermr/openVirus/issues/55#issuecomment-632161205, or unsubscribe https://github.com/notifications/unsubscribe-auth/APUV3XDAOYYEHBLMFSUZ32LRSVDCLANCNFSM4NGYIWMQ .

petermr commented 4 years ago

You will use the flags -k 100, -x, -p, `-o

.

Follow the TIGR2ESS tutorial for getpapersif you want an example.

vaishaliarora277 commented 4 years ago

SCREENSHOT

getpapers error: 'no output directory given'

Priya-Jk-15 commented 4 years ago

@vaishaliarora277 you should say the path/directory that the files need to get downloaded in your system. So use -o <directory name> along with your syntax.

You can refer the use of -o command using the syntax getpapers --help

petermr commented 4 years ago

Thanks! Great to see newcomers being helped!

-- Peter Murray-Rust Founder ContentMine.org and Reader Emeritus in Molecular Informatics Dept. Of Chemistry, University of Cambridge, CB2 1EW, UK