Problem running Medrxiv in windows 10

[Priya-Jk-15]

After downloading python and pip from

https://github.com/petermr/openVirus/blob/ferret/ferret/README.md

I am unable to download the requirements from the given syntax.

What shall I change in the syntax or is there anything else I should do before downloading the requirements?

Kindly guide me.

[petermr]

When we post Issues we have to take a special approach. It's like writing a record of an experiment. We have to make it clear (including printouts/console logs/files created, etc).

• what we were trying to do (including any instructions)
• what we expected to happen
• what actually happened (including error messages)
• (possibly) where we think the problem lies

For example:

• I'm running Ferret (On Windows-10) to query medrxiv
• I have installed Ferret and tested that it works (give output)
• I issued the following command (give details)
• I got the output (give details)
• the output file (name) does not contain any content

Or

• I have installed Ferret
• I cannot find documentation on how to issue a query

Or

• I have installed Ferret
• I ran a query against medrxiv (give details)
• after 20 minutes there was no output.

Or

• when trying to install Ferret I got a fatal error "no such class exception" (give full output).

It's perfectly OK to ask questions but they must be clear and they must show that you have tried to solve it as far as you can. (I'll give an example in Slack).

[Priya-Jk-15]

I am trying to run Medrxiv using the Dockerised Ferret Service

I have downloaded python and pip

I have installed ferret and
in ferret.exe, I gave the following command

pip install -r requirements.txt

The output shown was:

line 1:4 missing '(' at 'install'
Failed to parse the query
missing '(' at 'install' at 1:4

https://drive.google.com/file/d/1bV7asWnlWAgSQYHFguDcH7FT3CKpC2rK/view?usp=sharing

Did I give the command in correct directory?
Kindly help me in testing the installation of ferret and in downloading the requirements.

[petermr]

This is a good report @Priya-Jk-15 . If it's not too large, it would be useful to dislay the contents of requirements.txt.
Also useful to show which directory you launched this from.
(BTW this type of problem is quite common in installing and running new software)

[l-hawizy]

hi @Priya-Jk-15 , for the dockerised ferret, you don't need to run ferret.exe (ferret.exe is just for a local run of ferret)
You would just need to:

• go to where openVirus/ferret is installed using your terminal/cmd prompt
• make sure python3 is installed (run python --version)
• make sure pip is installed
• run pip install -r requirements.txt

[Priya-Jk-15]

I have installed python and pip, and tested its installation.

python --version
python 3.8.2

pip --version
pip 20.1.1

but
I haven't installed Docker , so to run Ferret locally:

I think I have installed Ferret
In ferret.exe ,its shown like this

Welcome to Ferret REPL 0.11.1
Please use `exit` or `Ctrl-D` to exit this program.
>

By the instructions, from
https://github.com/petermr/openVirus/blob/ferret/ferret/README.md
after installation of ferret, set an alias for the ferret variable by the command

alias ferret="path/to/ferret/directory"

I am confused whether should I pass the command in command prompt or in ferret.exe ?

[ziflex]

I have installed python and pip, and tested its installation.

python --version
python 3.8.2

pip --version
pip 20.1.1

but
I haven't installed Docker , so to run Ferret locally:

I think I have installed Ferret
In ferret.exe ,its shown like this

Welcome to Ferret REPL 0.11.1
Please use `exit` or `Ctrl-D` to exit this program.
>

By the instructions, from
https://github.com/petermr/openVirus/blob/ferret/ferret/README.md
after installation of ferret, set an alias for the ferret variable by the command

alias ferret="path/to/ferret/directory"

I am confused whether should I pass the command in command prompt or in ferret.exe ?

When you just execute ferret.exe without any arguments - you get into REPL mode that allows you to type and execute commands.
If you want to execute a particular query from a file, you should provide a path to the file:

ferret.exe myquery.fql

You might want to add an additional parameter to ferret.exe:

ferret.exe --cdp-launch myquery.fql

This will launch Chrome in headless mode in order to scrape interactive web pages.