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1.1. Installing for Linux (Production)

Paulo Pinheiro edited this page Jan 8, 2021 · 8 revisions

Important Note

Commands in this section are root commands and should be preceded with sudo if current user is not root

Overview

A basic HADatAc installation involves the following five steps:

  • acquiring required software for installing/running the HADatAc Console

  • downloading HADatAc code from this GitHub repository

  • deploying HADatAc database dependencies

  • deploying HADatAc

  • proxy setting

Step 1 : Acquiring Required Software

Before anything, however, we need to verify that the host machine has a git client to retrieve the code, and an sbt utility to run the console. In the command line of your machine, verify that you have a git client installed in your machine:

git

If you do not have git, you need to install one: http://git-scm.com/downloads. Still from the command line, verify that you have sbt applications installed in your machine:

sbt

If not, you need to install one: http://www.scala-sbt.org/.

You will also need:

  1. Java JDK 8: http://java.com/en/download/ (or use your distribution's java) (MAKE SURE THE MACHINE IS NOT RUNNING JAVA 9)
  2. wget

Step 2: Cloning HADatAc Code

The commands in this section are to be issued by root user

Create both /data and /data/git folders:

  mkdir -p /data/git

Go to git directory :

  cd /data/git

Once your are in your home directory (~ is a shortcut for your home directory), clone HADatAc code by typing the following command:

  git clone https://github.com/paulopinheiro1234/hadatac.git

After cloning HADatAC, you should have a hadatac folder under your home directory. Go into the hadatac directory under your home directory by typing the following:

 cd /data/git/hadatac

Step 3: Deploying HADatAc Database-dependencies

Once you are in /data/git/hadatac (you can check if you are in the right folder by typing pwd), type the following:

  ./production_install_hadatac.sh

Note: use chmod a+x *.sh if the script above cannot be executed

This process will take a while so let it run. It will download and install a SOLR instance, a Blazegraph instance, and initialize the instance.

During the process of executing the script, you will be asked for an installation folder. Use /data/hadatac as installation folder

Open your browser to verify if the SOLR installation was successful

Open your browser to verify if the Blazegraph installation was successful

Once inside Blazegraph's web page (link above), select the 'Namespaces' tab, and verify if the required namespaces store, store_sandbox, and store_users have been created.

Step 4: Deploying HADatAc

Go back to hadatac folder:

 cd /data/git/hadatac

Now type the following:

 ./deploy_hadatac.sh

Browser open hadatac url: http://localhost:9000/hadatac/

Wait for page to open, it will take a while.

Step 5. Setting up proxy configuration

In the instruction below we use apache2 for proxying hadatac from localhost:9000 into (domain)/hadatac

Assuming that apache2 is installed, change to apache2 folder in /etc

 cd etc/apache2

in the /sites-available folder, edit the conf file. Look for

<VirtualHost *:80>

Right before the closing tag </VirtualHost>, add the following content:

 ProxyRequests Off

 <Proxy *>
     Order deny,allow
     Allow from all
 </Proxy>

 ProxyPass /hadatac http://127.0.0.1:9000/hadatac
 ProxyPassReverse /hadatac http://127.0.0.1:9000/hadatac

Save the file.

Go to http://(domain)/hadatac, where (domain) is the name of your domain

Data Owner Guide

  1. Installation
    1.1. Installing for Linux (Production)
    1.2. Installing for Linux (Development)
    1.3. Installing for MacOS (Development)
    1.4. Deploying with Docker (Production)
    1.5. Deploying with Docker (Development)
    1.6. Installing for Vagrant under Windows
    1.7. Upgrading
    1.8. Starting HADatAc
    1.9. Stopping HADatAc
  2. Setting Up
    2.1. Software Configuration
    2.2. Knowledge Graph Bootstrap
    2.2.1. Knowledge Graph
    2.2.2. Bootstrap without Labkey
    2.2.3. Bootstrap with Labkey
    2.3. Config Verification
  3. Using HADatAc
    3.1. Initial Page
    3.1.1. Home Button
    3.1.2. Sandbox Mode Button
    3.2. File Ingestion
    3.2.1. Ingesting Study Content
    3.2.2. Manual Submission of Files
    3.2.3. Automatic Submission of Files
    3.2.4. Data File Operations
    3.3. Manage Working Files 3.3.1. [Create Empty Semantic File from Template]
    3.3.2. SDD Editor
    3.3.3. DD Editor
    3.4. Manage Metadata
    3.4.1. Manage Instrument Infrastructure
    3.4.2. Manage Deployments 3.4.3. Manage Studies
    3.4.4. [Manage Object Collections]
    3.4.5. Manage Streams
    3.4.6. Manage Semantic Data Dictionaries
    3.4.7. Manage Indicators
    3.5. Data Search
    3.5.1. Data Faceted Search
    3.5.2. Data Spatial Search
    3.6. Metadata Browser and Search
    3.7. Knowledge Graph Browser
    3.8. API
    3.9. Data Download
  4. Software Architecture
    4.1. Software Components
    4.2. The Human-Aware Science Ontology (HAScO)
  5. Metadata Files
    5.1. Deployment Specification (DPL)
    5.2. Study Specification (STD)
    5.3. Semantic Study Design (SSD)
    5.4. Semantic Data Dictionary (SDD)
    5.5. Stream Specification (STR)
  6. Content Evolution
    6.1. Namespace List Update
    6.2. Ontology Update
    6.3. [DPL Update]
    6.4. [SSD Update]
    6.5. SDD Update
  7. Data Governance
    7.1. Access Network
    7.2. User Status, Categories and Access Permissions
    7.3. Data and Metadata Privacy
  8. HADatAc-Supported Projects
  9. Derived Products and Technologies
  10. Glossary
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