pif-ingestor

Script to ingest common data formats to citrination. It uses an extention architecture to import and evaluate converters defined in other pacakages, e.g. pif-dft and sparks-pif-converters.

Installation

Install this ingestor and all known public converters:

$ pip install pif-ingestor[all]

This will place an executable pif-ingestor in your bin directory (or the bin directory of your virtualenv).

Known public converters

• dfttopif (ingests VASP and Quantum Espresso calculations)
• csv_template_ingester (ingests CSV files with PIF field information in the header)

Usage

$ usage: pif-ingestor [-h] [-f FORMAT] [-r] [-d DATASET]
                    [--tags TAGS [TAGS ...]] [-l LICENSE] [-c CONTACT]
                    [-z ZIP] [-t TAR] [--globus-collection GLOBUS_COLLECTION]
                    [-m META] [--args CONVERTER_ARGUMENTS]
                    path

Ingest data files to Citrination

positional arguments:
  path                  Location of the file or directory to import

optional arguments:
  -h, --help            show this help message and exit
  -f FORMAT, --format FORMAT
                        Format of data to import, coresponding to the name of
                        the converter extension
  -r, --recursive       Recursively walk through path, ingesting all valid
                        subdirectories
  -d DATASET, --dataset DATASET
                        ID of the dataset into which to upload PIFs
  --tags TAGS [TAGS ...]
                        Tags to add to PIFs
  -l LICENSE, --license LICENSE
                        License to attach to PIFs (string)
  -c CONTACT, --contact CONTACT
                        Contact information (string)
  -z ZIP, --zip ZIP     Zip to this file
  -t TAR, --tar TAR     Tar to this file
  --globus-collection GLOBUS_COLLECTION
                        Globus Publish collection to upload files
  -m META, --meta META  Meta-data in common format
  --args CONVERTER_ARGUMENTS
                        Arguments to pass to converter (as JSON dictionary)

Examples

Convert a VASP file, generating a quality report, and upload it to datasetID 7:

$ pif-ingestor B.hR12 -f dft -d 7 --args='{"quality_report" : true}'

Support

For users: check out the citrination-users google group.

For developers: use issues and pull requests.