ncmirtools 0.5.2

Set of commandline tools for NCMIR

ncmirtools

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

For more information please visit our wiki page:

https://github.com/CRBS/ncmirtools/wiki

Tools

• mpidir.py – Given a Microscopy product id, this script finds the path on the filesystem

• projectdir.py – Given a project id, this script finds the path on the filesystem

• projectsearch.py – Allows caller to search database for projects

• mpidinfo.py – Queries database and returns information on specific Microscopy Product

• imagetokiosk.py – Transfers second youngest image file to remote server via scp

• ncmirtool.py – 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)

Dependencies

• argparse

• configparser

• pg8000

• ftpretty

• paramiko

Compatibility

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

Installation

Try one of these:

pip install ncmirtools

python setup.py install

License

See LICENSE.txt

Bugs

Please report them here

Credits

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

History

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 ncmirtool.py cilupload Issue #17

• Created ncmirtool.py to prototype a single command line script entry point. Issue #13

• Dropped support for Python 2.6

0.4.0 (2017-06-28)

• Added imagetokiosk.py 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 mpidinfo.py script to provide information about Microscopy Product from database. Issue #6

• Fixed bug in mpidinfo.py where passing id greater then 2^31 -1 resulted in uncaught ProgrammingException Issue #9

• Consolidated all _setup_logging() calls into one function in config.py. 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 projectdir.py script which finds directories for a given project id. Issue #3

• Added projectsearch.py 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 mpidir.py