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Step by Step manual to Setup SciCat without Containers

Setup Backend (catamel)

Mongo

The first part is to setup a Mongo DB, if not yet existing. You will need at least version 3.4 . In the simplest case a simple

yum install mongodb-server

(on RedHat systems) or similar will suffice.

A production ready setup however may require to setup a replicated DB server. Follow the Mongo DB Manuals in this case. E.g. at PSI we operate a 3 fold relicated Mongo DB server.

Hint to add full text indexing

Mongo DB needs to work with Indices to speed up the queries. All of these index definitions are created automatically, with one exception. This exception is described here: the following command must be executed after the database has been created in MongoDB, i.e. after starting catamel once.

Log into mongodb at the console, e.g. run

  1. If not using Kubernetes
mongo dacat

or, if using Kubernetes

kubectl exec -it <mongo container> mongo dacat

and enter

db.Dataset.createIndex( { "$**": "text" } )

Note: If the index is not created as above, catanie e2e test fails.

API Server

Prerequisites

First you need to have node/npm installed

npm version 6 or higher
Node version 10 or higher

The needed database will be created automatically when the API server starts.

Get code

git clone https://github.com/SciCatProject/catamel.git
cd catamel
git checkout master # (or develop)
npm install

Please note: the master branch is often quite behind the development, therefore to get all new features you may want to use the develop branch instead.

Setup configuration

There are 5 configuration files that need to be adjusted to your situation. There are example configuration files for each of the 4 configuration files inside the server directory

  1. functionalAccounts.json : defines the functional accounts, such as admin, ingestor etc
  2. datasources.json : defines the connection to the Mongo DB -sample datasources.json
  3. providers.json : defines the authentication source for user accounts, e.g. how to link to your local LDAP/AD server
  4. config.local.js : defines the API server details, API root address, your local site name and policy settings for , the PID prefix for your datasets, the type of message broker to use, the connection to an email send server etc
  5. component-config.json: defines the Express framework components, in particular if the explorer is enabled and optionally definition of the RabbitMQ topology, if used.

Adjusting these settings to your infrastructure should be straight forward. In case you do not understand a setting just leave it at its default.

Start metadata server

npm run start

Test functionality

npm run test

You can inaddition test the API server using the "explorer", e.g if you run the instance locally point your browser to https://localhost:3000/explorer (note the explorer might be disabled for production environments, check the component-config.json file)

API Explorer

You can use this web interface to test all the available API end points. If you test endpoints, which are protected by authentication, then you first need to login , get an accessToken and fill it into the accessToken field on top of the explorer web page

Setup GUI frontend

These instructions will get you a copy of the project up and running on your local machine for development and testing purposes. See deployment for notes on how to deploy the project on a live system.

Prerequisites

What things you need to install the software and how to install them

Angular v8 or higher
npm version 6 or higher
node version 10 or higher

Installing

Use git to clone the repository

git clone https://github.com/SciCatProject/catanie
cd catanie

First install the required modules

npm install

Then build with the Angular CLI

npx ng build

You can deploy a test server with the following command:

npx ng serve

Running the unit tests

To run the unit tests, type:

npm test

End to end tests

To run the end to end tests, type:

npm run e2e

Configuration

You can fine tune the features that you want to use in the GUI by setting the flags inside the src/environments folder. In this folder you find several example configuraion files used by the Sites. Please adjust to your needs. The angular.json file contains a section "configurations" which defines a set of prepared configurations, that you can choose from. This defines which files will be picked up at build time. The build system defaults to the environment.ts, but if you e.g. do ng build --env=development then environment.development.ts will be used instead. Here is an example configuration file

The most important configuration setting is the connection to the API server

lbBaseURL: "https://your-loopbak-api-server",

Many of the other settings are boolean flags, which allow you to switch on/off features of the GUI Again, if in doubt, just leave the setting as defined in the available example environment files or leave them empty.

TODO Add local TOC at start of each longer honkit page