Archive | May, 2013

Clarity LIMS API Integrations

Improvements to the EPP Smoke Test

Introduction In an earlier post, I’d created a short script to test that EPP nodes were working. The script was painfully simple, and provided a file whose contents was date-stamped with the date/time that the script ran, and the file was captured in the normal manner, and displayed in the genealogy. After receiving feedback from […]

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Clarity LIMS API Integrations

Attaching Files Programatically

Did you know there are four places in which files can be attached to the GenoLogics LIMS? We probably all know that files can be attached to ResultFile placeholders in the genealogy, and also attached to Projects (Sample Submission Spreadsheets for example), but files can also be attached to Samples and Processes. These latter two […]

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Clarity LIMS API Integrations

Further Uses of the EPP Wrapper Script

In an earlier blog posting, I described the use of a Python ‘wrapper’ script. Its initial use was to enable a single Process to initiate two (or more!) external applications. I recently stumbled across an issue that I solved using the ‘wrapper’, and thought I’d post my findings. First of all, let’s refresh our memory […]

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Clarity LIMS API Integrations

Testing the EPP Plugin

Background With many Rapid Scripting API customers having multiple test systems there is often a need to test quickly if the associated EPP node is correctly installed and configured. To this end I created a script that can be run from a sample or a file in order to test the underlying plumbing, without the […]

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Clarity LIMS API Integrations

Creating an EPP Wrapper Script With Python

Background Most facilities have the need for the LIMS to initiate an external application or algorithm as a consequence of a user completing an operation within the desktop client. This functionality requires the use of the GenoLogics External Program Plugin (EPP), which associates a Process with the command line syntax required to drive the external […]

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Summary of the Asia Pacific Illumina Scientific Summit: MIcrobiome and NGS

Summary of the Asia Pacific Illumina Scientific Summit

After a whirlwind of spring conferences and U.S. and European Illumina User Group Meetings we rounded out our April with the Illumina Asia Pacific Summit on the beautiful Phuket Island in Thailand. The summit provided presentations on an exciting variety of topics including: the ENCODE project and recent findings on regulatory elements, ovarian cancer and […]

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