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Documentation of getpapers & ami

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Radhu Ladani edited this page Jan 15, 2021 · 5 revisions

getpapers

getpapers is a simple, powerful tool for querying repositories of scholarly articles using a simple one-line command.

Name: Radhu Ladani

Operating System: Windows 10

a. Downloading & Installation of node

  • Open the windows-nvm repository in your internet browser.
  • Download the nvm-setup.zip file for the most recent release.
  • Once downloaded, open the zip file, then open the nvm-setup.exe file.
  • The Setup-NVM-for-Windows installation wizard will walk you through the setup steps, including choosing the directory where both nvm-windows and Node.js will be installed.
  • Once the installation is complete. Open Command Prompt and try using windows-nvm to list which versions of Node are currently installed (should be none at this point): nvm ls
  • Install the current release of Node.js (for testing the newest feature improvements): nvm install latest
  • Install the latest stable LTS release of Node.js (recommended) by first looking up what the current LTS version number is with: nvm list available, then installing the LTS version number with: nvm install <version> (replacing <version> with the number, ie: nvm install 12.14.0).
  • List what versions of Node are installed: nvm ls now you should see the two versions that you just installed listed.
  • After installing the Node.js version numbers you need, select the version that you would like to use by entering: nvm use <version> (replacing <version> with the number, ie: nvm use 12.9.0).
  • Verify which version of npm is installed with: npm--version, this version number will automatically change to whichever npm version is associated with your current version of Node.js.

b. Installation of getpapers

Source of Instruction: ContentMine / getpapers

Steps in the Installation:

  1. Open Comand Prompt
  2. Run the command npm install --global getpapers

Installation: Successful

Test of the Installation:

  1. Type getpapers in Command Prompt.
  2. Usage and options displayed.

c. Usage of getpapers

The tool was used to retrieve 200 papers on the topic, 'embelia ribes' with the output directory specified as 'example'.

Command used: getpapers -q 'embelia ribes' -k 200 -o example

Results

  1. A new directory (example) created within the home directory.
  2. 200 folders (PMC###) created within 'example' each containing a JSON file (eupmc_result).
  3. 1 text file (eupmc_fulltext_html_urls) containing the URLs of all downloaded documents.
  4. 1 JSON file (eupmc_results) created.

Command line output

  1. 0 error messages.
  2. 2 warnings (warn: This version of getpapers wasn't built with this version of the EuPMC api in mind; warn: getpapers EuPMCVersion: 5.3.2 vs. 6.5 reported by api).

ami

ami is a framework for gathering, searching, transforming scholarly publications, oriented towards STEMM (Science, technology, Engineering, Medicine, Maths).

Installation of ami

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 java 13.0.2
  • Test the installation by giving the command java -version in command prompt

2. Install latest JDK

3. 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 command prompt

4. Install maven

  • 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 --help and if ami is installed the commands to be used for ami are listed.
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