Skip to main content

Migrate older EMDB-SFF files to newer versions

Project description

https://badge.fury.io/py/sfftk-migrate.svg PyPI - Python Version https://travis-ci.org/emdb-empiar/sfftk-migrate.svg?branch=master Documentation Status https://coveralls.io/repos/github/emdb-empiar/sfftk-migrate/badge.svg?branch=master

About

sfftk-migrate is a utility for migrating EMDB-SFF files from older to the latest version of the data model (see https://emdb-empiar.github.io/EMDB-SFF/ for the latest version). It currently only supports migrations of XML (.sff) files from EMDB-SFF v0.7.0.dev0.

Usage

The main entry point for this utility is the sff-migrate command. Please consult the command-line help using:

~$ sff-migrate -h
usage: sff-migrate [-h] [-t TARGET_VERSION] [-o OUTFILE] [-v] [-l] [-s]
                   [infile]

Upgrade EMDB-SFF files to more recent schema

positional arguments:
  infile                input XML file

optional arguments:
  -h, --help            show this help message and exit
  -t TARGET_VERSION, --target-version TARGET_VERSION
                        the target version to migrate to [default: 0.8.0.dev1]
  -o OUTFILE, --outfile OUTFILE
                        outfile file [default: <infile>_<target>.xml]
  -v, --verbose         verbose output [default: False]
  -l, --list-versions   list supported versions [default: False]
  -s, --show-version    show the version of the input file [default: False]

Migrating is simple:

~$ sff-migrate file.sff

List supported versions:

~$ sff-migrate -l
versions migratable to 0.8.0.dev1:
* 0.7.0.dev0

Show the file’s version:

~$ sff-migrate -s sfftk_migrate/data/xml/emd_1547.sff
file sfftk_migrate/data/xml/emd_1547.sff is of version 0.7.0.dev0

~$ sff-migrate -s sfftk_migrate/data/xml/emd_1547_v0.8.0.dev1.sff
file sfftk_migrate/data/xml/emd_1547_v0.8.0.dev1.sff is of version v0.8.0.dev0

License

sfftk-migrate is free and open source software released under the terms of the Apache License, Version 2.0. Source code is copyright EMBL-European Bioinformatics Institute (EMBL-EBI) 2020.

Source code is available from the Github repository: https://github.com/emdb-empiar/sfftk-migrate

Project details


Download files

Download the file for your platform. If you're not sure which to choose, learn more about installing packages.

Files for sfftk-migrate, version 0.1.0b7
Filename, size File type Python version Upload date Hashes
Filename, size sfftk_migrate-0.1.0b7-py3-none-any.whl (32.3 kB) File type Wheel Python version py3 Upload date Hashes View
Filename, size sfftk-migrate-0.1.0b7.tar.gz (19.1 kB) File type Source Python version None Upload date Hashes View

Supported by

AWS AWS Cloud computing Datadog Datadog Monitoring DigiCert DigiCert EV certificate Facebook / Instagram Facebook / Instagram PSF Sponsor Fastly Fastly CDN Google Google Object Storage and Download Analytics Microsoft Microsoft PSF Sponsor Pingdom Pingdom Monitoring Salesforce Salesforce PSF Sponsor Sentry Sentry Error logging StatusPage StatusPage Status page