LabCollector Advanced Search Manager with Elasticsearch – LabCollector

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LabCollector Advanced Search Manager with Elasticsearch

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SUMMARY:

LabCollector has released new add-on called “Advanced Search Manager” that enables more searching options in LabCollector with the help of Elasticsearch. Its distributed architecture makes it possible to search and analyze huge volumes of data in near real time. It allows you to store, search, and analyze big volumes of data quickly and in near real time. It is generally used as the underlying engine/technology that powers applications that have complex search features and requirements.

LabCollector can integrate Elasticsearch to empower search functionalities.

Phase 1: limited to ELN
Phase 2: added to LabCollector inventory/LIMS
Phase 3: added to more addons

Follow the bellow steps to understand & perform search with Advanced search add-on:

1. Functionalities and logic

2. Requirements

3. Installation

1. Functionalities and logic

  • Elasticsearch takes in unstructured data from different locations, stores and indexes it, according to user-specified mapping (which can also be derived automatically from data) and makes it searchable.
  • Indexes are used to quickly locate data without having to search every row in a database table every time a database table is accessed.
  • LabCollector will handle all needed indexing of data and files to Elasticsearch engine.

2. Requirements

  • PHP v7.2.5+
  • Elasticsearch v7.x (*Module at actual state will not be compatible with v8 due to Elasticsearch API system)
  • Elasticsearch’s Ingest Attachment Processor Plugin is required
  • LabCollector v6.01+ and ELN v4.03+
  • Advanced Search Management add-on

3. Installation

  • Elasticsearch can be installed on same server of LabCollector OR on a dedicated server/VM or use an Elasticsearch cloud service (AWS, Elasticcloud…). See diagram in section 1.
  • Installation of Elasticsearch is done according to your server OS and it is very easy.
  • Please follow the guide described below:
    • Go to https://www.elastic.co/guide/en/elasticsearch/reference/current/install-elasticsearch.html
    • After installation go to Advanced search Manager add-on -> Settings
      *below is an example image where some settings are preconfigured before that is why you see some index list.

    • In the settings you need to define define a storage location for the indexes.
      *LabCollector will handle all needed indexing of data and files to Elasticsearch engine.
    • Default port is 9200.
      *A username & password can be defined too, if needed.
    • Once done “Update” the settings to Configure Advanced search add-on to connect to the newly installed Elasticsearch
    • Ex:

  • Once the above process is done you need to define indexing CRON:
    Cron is a standard Unix utility that is used to schedule commands for automatic execution at specific intervals. 
  • To define CRON task go to the Homepage of the Advanced search Manager add-on.
    *Below is an example of CRON task for already created ELN Elastic search.

  • When you click on the Cron task, you will see the below pop-up, where you can define the task frequency (hours, minutes) and task time (24 hours)

  • Once you add the task you will see the message below.

  • Create index by going to options icon.
    *Below is an example of CRON task for already created ELN Elastic search.

  • If your connections good you will see the below message.