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.  "auto" will try installed
                        ingesters until one works.  "merge" will try all 
                        installed ingesters and try to merge the results into
                        a single PIF.
  -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.