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INSTALLING.md

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Installation and use

getpapers

See https://github.com/ContentMine/getpapers for instruction. You will need Node installed (instructions included).

ami

Needs Java 8 or higher. Two approaches:

Download and run jars

build with Maven or IDE

Code on https://github.com/petermr/ami3/ . to clone this use

git clone https://github.com/petermr/ami3.git

and then build with:

cd <ami3 directory>
mvn install -Dmaven.test.skip=true

This gives an executable in <your dir>/ami3/target/appassembler and you should set your PATH to include <your dir>/ami3/target/appassembler/bin

ADVANCED

Using Docker

Building your own image

This repository comes with a Dockerfile which builds the required environment (ami3, jdk8, node). This build and these instructions are heavily influenced by the Dockerfile for ami3 itself.

To build the image yourself (assuming you have docker installed and running), you can use:

docker build --tag openvirus .

Running this image puts you into a bash environment with access to the AMI binaries:

$ docker run --rm -it openvirus
root@3174f53a42c0:/workspace# ami-pdf --help
Usage: ami-pdf [OPTIONS]
Description
===========
Convert PDFs to SVG-Text, SVG-graphics and Images. Does not process images,
[...]

You can also mount your current directory and execute commands on your own data:

docker run --rm -it -v $(pwd):/workspace openvirus ami-image example.jpg

Pulling pre-built images from Docker Hub

For the time being (23/03/2020), if you just want to pull a pre-built image, you can do so via

docker pull mlevs/openvirus

There is no guarantee that this image will remain at this location on Docker Hub, you should verify the image looks sensible at mlevs/openvirus on Docker Hub.

Building from source

Initially we use the command line and well-known systems (Java, R, Text-editing).

AMI

The AMI system is a set of about 20 linked command-line tools for creating an AMI "CProject" - a set of directories with defined names and functions. For a tutorial see https://github.com/petermr/tigr2ess/tree/master/installation (which might be slightly out of date; if so please copy here and amend).

Ideally you should be able to checkout and compile Java under Maven. This creates a single deployable jar file with a series of scripts to run under unix/macosx or Windows.

JDK

install a Java JDK on your machine (JDK8 or higher)

Suggest https://howtodoinjava.com/maven/how-to-install-maven-on-windows/ or https://www3.ntu.edu.sg/home/ehchua/programming/howto/JDK_Howto.html

Verify by typing:

javac

which should give help.

Maven

Install maven

https://maven.apache.org/install.html

checkout ami3

cd to where your software (will) live.

git clone https://github.com/petermr/ami3.git

should create ami3/

cd ami3

there should be a file pom.xml

mvn

compile and install with

mvn install -Dmaven.test.skip=true

this should create a file ami3/target/appassembler/

run

The files in ami3/target/appassembler/bin represent commands

Thus (on my machine) /Users/pm286/workspace/cmdev/ami3/target/appassembler/bin//ami-section

will run ami-section.

Normally you will add <mysoftware>/ami3/target/appassembler/bin/ to your CLASSPATH where <mysoftware> is the ami3 directory.

https://docs.oracle.com/javase/tutorial/essential/environment/paths.html