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Convert New York University specimen tables to ERNE cache database format

Project description

This is a converter. It takes specimen records from New York University Medical School (NYU)’s cancer research specimen collection that are stored as a series of spreadsheets. From those, it outputs a series of SQL statements that can be injected into the cache system of the Early Detection Research Network (EDRN) Resource Network Exchange (ERNE).

That lets the EDRN public portal show the specimens collected at NYU, without requiring an ERNE server to be installed at NYU.

Nifty, huh?

Requirements

This package has no external requirements (aside from Python >=2.4 <3.0).

Installation

By far, the easiest way to install the NYU XLS to ERNE Converter is to use pip or easy_install. As a privileged user, type:

pip install edrn.nyuxls2erne

or:

easy_install edrn.nyuxls2erne

The software as well as its dependencies will be downloaded and installed automatically.

Are you an advanced user who takes advantage of virtualenv or buildout? You know what to do.

Installing from Source

If neither pip nor easy_install are available on your system, just install from source:

  1. Download the source package archive.
  2. Extract the gzip’d tar archive.
  3. In the extracted directory, run python setup.py install as a privileged user.

Changelog

What follows is a history of changes from release to release, along with issues addressed and new features in each release.

0.0.2 — Check Out Those Lungs

This release addresses the following issue:

  • CA-832 - Correct NYU Specimen Site, PI and Organ

0.0.1 — Codename: Maureen Colbert

This release addresses the code interpretation issue identified in https://edrn-jpl.basecamphq.com/W4242569 and codenamed “Maureen Colbert” because of the subject line of the email message that the project investigator replied to in order to push these changes into effect.

This release also adds the mkrelease utility to its buildout in order to simplify future releases.

0.0.0 — Unreleased

There are no releases yet of the NYU XLS to ERNE converter.

Issue Tracker

The issue tracker is located at https://oodt.jpl.nasa.gov/jira/browse/CA.

Project details


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