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Set of commandline tools for NCMIR

Project description


Pypi Updates Code issues

Set of commandline tools for interaction with data hosted internally at NCMIR.

For more information please visit our wiki page:


  • – Given a Microscopy product id, this script finds the path on the filesystem
  • – Given a project id, this script finds the path on the filesystem
  • – Allows caller to search database for projects
  • – Queries database and returns information on specific Microscopy Product
  • – Transfers second youngest image file to remote server via scp
  • – New tool that will soon be the main entry point for all commands above. Currently offers prototype uploading of data to Cell Image Library (CIL)


  • Should work on Python 2.7, 3.3, 3.4, & 3.5 on Linux distributions


Try one of these:

pip install ncmirtools

python install




Please report them here


This package was created with Cookiecutter and the audreyr/cookiecutter-pypackage project template.


0.5.2 (2018-04-02)

  • Another fix for Issue #18 where the path output to standard out had incorrect path delimiter output.

0.5.1 (2018-04-02)

  • Set delimiter for uploads to / to deal with problem uploading files from windows machine. Issue #18

0.5.0 (2018-03-28)

  • Created prototype cilupload tool. Accessible via cilupload Issue #17
  • Created to prototype a single command line script entry point. Issue #13
  • Dropped support for Python 2.6

0.4.0 (2017-06-28)

  • Added which transfers second youngest image file to remote server via scp. Issue #16
  • Fixed a couple minor issues so this tool will work on Windows. Issue #14

0.3.0 (2017-01-13)

  • Added script to provide information about Microscopy Product from database. Issue #6
  • Fixed bug in where passing id greater then 2^31 -1 resulted in uncaught ProgrammingException Issue #9
  • Consolidated all _setup_logging() calls into one function in Issue #8
  • Modified NcmirToolsConfig to look for configuration file in /etc/ncmirtools.conf as well as the users home directory Issue #7

0.2.0 (2016-11-8)

  • Added script which finds directories for a given project id. Issue #3
  • Added script which given a string will search a postgres database for projects with that string in the name or description.

0.1.1 (2016-10-14)

  • Minor improvements to README.rst for better presentation on pypi

0.1.0 (2016-10-04)

  • Initial release with single script

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