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INSTALLING ami3

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kareenasingh edited this page Jun 12, 2020 · 21 revisions

installation

There are two methods. If you are developing ami3 you should use the first. If you are doing production runs and not Maven-savvy then use the second JAR-file route

maven / IDE

If you can compile and run under maven and/or Eclipse/IntelliJ/Netbeans that's the most powerful way.

There are a lot of tests and a lot of them are out of date and fail, so we suggest

git clone https://github.com/petermr/ami3.git
cd ami3
mvn install -Dmaven.test.skip=true

That will build ami3/target/appassembler/bin and ami3/target/appassembler/repo The exes are in the first. If your PATH contains this, then you can run ami commands. My path includes:

/Users/pm286/workspace/cmdev/ami3/target/appassembler/bin/

(Note that if you rebuild with maven or maven clean this dir gets wiped and overwritten by a new version.)

Single JAR method

Download the latest JAR from https://github.com/petermr/ami-jars3 NOTE CHANGED REPO. They are in dated directories, probably every few days. Use new ones if bugs are fixed or new features are added that you need.

General instructions.

see https://github.com/petermr/tigr2ess/blob/master/installation/INSTALLATION.md

This is a year old. It should be roughly accurate. PLEASE copy to openVirus and update if necessary

Alpha Tester:

Name: Ambreen Hamadani

Installation

  1. Downloaded and installed JDK from Oracle(https://www.oracle.com/java/technologies/javase-jdk14-downloads.html)
  2. Downloaded and installed maven (https://maven.apache.org/install.html)
  3. Cloned the ami3 from Github and added it to path as suggested above.
  4. Tested its installation by running ami --help
  5. Installation successful (0 errors, 0 warnings)

Usage

Reference Tutorial](https://github.com/petermr/openVirus/blob/master/examples/n95/OVERVIEW.md)

  1. An attempt was made to run ami3 on 100 viral epidemic papers using country disease funders dictionaries.
  2. getpapers was used to create directory and the respository of papers: getpapers -q "viral epidemics" -o ami_test_1 -f v_epid/log.txt -x -p -k 100
  3. The directory, ami_test_1 was used as CProject directory for ami3: ami -p ami_test_1 search --dictionary country disease funders
  4. 17 new files got created within ami_test_1 ( 12 XML, 1 folder, 4 HTML)
  5. 0 Errors, multiple warnings like: Warning at procedure xsl:unnamed on line 0 XTDE0540 Ambiguous rule match for /article/front[1]/journal-meta[1]

Tester 2

Name: Kareena Singh

Steps of installation

  1. Install Java
  • You can download and install java using https://java.com/en/download/
  • Make sure you have the latest version, in my case version 1.8
  • Test the installation by giving the command java -version in your command prompt and you will get java version "1.8.0_251"
  1. Install latest JDK
  1. Install git
  • Download and install latest git using https://git-scm.com/downloads
  • Launch git bash
  • Test the installation by giving the command git -version in your command prompt and you will get git version 2.27.0.windows.1
  1. Install maven
  • Download and install maven using https://maven.apache.org/install.html
  • Extract all files
  • Set path variable
  • Test installation using mvn -version and you will get apache maven version 3.6.3
  1. Open your command prompt and enter the following commands
git clone https://github.com/petermr/ami3.git
cd ami3
mvn install -Dmaven.test.skip=true

This will let you install and build ami

  • Test your installation using ami-pdf

Issues faced during installation

  1. Error: 'ami' is not recognized as an internal or external command, operable program or batch file.
  • Make sure you have set path variables for jdk, maven and contentmine using the above links.

Usage of ami

  1. getpapers was used to create directory/folder and the repository of papers getpapers -q "viral epidemics" -o ami_test_2 -f v_epid/log.txt -x -p -k 100
  • This will create a CProject directory named as "ami_test_2"
  1. Now to search about your dictionary you can enter ami-pdf -p ami_test_2 search --dictionary viruses
  2. Output- 82 files created under the directory "ami_test_2" containing pdf, xml and images about my dictionary search All downloads succeeded.
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