pypfb 0.2.0

Python SDK for PFB format

# :construction: PFB Python SDK :construction:

Python SDK to create, explore and modify PFB (Portable Format for Biomedical Data) files.

## PFB Schema

[![metadata][1]][1]

## Installation

• From PyPI:

`bash pip install pypfb[gen3] `

(The optional gen3 dependencies add the ability to convert a Gen3 data dictionary into a PFB file.)

• From source code:

`bash pipenv install `

(Also add –dev for development.)

## Usage

### Main

Usage: pfb [OPTIONS] COMMAND [ARGS]…

PFB: Portable Format for Biomedical Data.

Commands:

add Add records into a PFB file. from Generate PFB from other data formats. make Make a blank record for add. rename Rename different parts of schema. show Show different parts of a PFB file. to Convert PFB into other data formats.

### Show different parts of PFB

Usage: pfb show [OPTIONS] COMMAND [ARGS]…

Show records of the PFB file.

Specify a sub-command to show other information.

Options:

-i, --input FILENAME

The PFB file. [default: <stdin>]

-n, --limit INTEGER

How many records to show, ignored for sub-commands. [default: no limit]

Commands:

metadata Show the metadata of the PFB file. nodes Show all the node names in the PFB file. schema Show the schema of the PFB file.

### Convert Gen3 data dictionary into PFB schema

Usage: pfb from [PARENT OPTIONS] dict DICTIONARY

Convert Gen3 data DICTIONARY into a PFB file.

If DICTIONARY is a HTTP URL, it will be downloaded and parsed as JSON; or it will be treated as a local path to a directory containing YAML files.

Parent Options:

-o, --output FILENAME

The output PFB file. [default: <stdout>]

### Convert JSON for corresponding datadictionary to PFB

Usage: pfb from [PARENT OPTIONS] json [OPTIONS] [PATH]

Convert JSON files under PATH into a PFB file.

Parent Options:

-o, --output FILENAME

The output PFB file. [default: <stdout>]

Options:

-s, --schema FILENAME

The PFB file to load the schema from. [required]

--program TEXT

Name of the program. [required]

--project TEXT

Name of the project. [required]

### Make new blank record

Usage: pfb make [OPTIONS] NAME

Make a blank record according to given NODE schema in the PFB file.

Options:

-i, --input PFB

Read schema from this PFB file. [default: <stdin>]

### Add new record to PFB

Usage: pfb add [OPTIONS] PFB

Add records from a minified JSON file to the PFB file.

Options:

-i, --input JSON

The JSON file to add. [default: <stdin>]

### Rename different parts of PFB (schema evolution)

Usage: pfb rename [OPTIONS] COMMAND [ARGS]…

Rename different parts of schema.

Options:

-i, --input FILENAME

Source PFB file. [default: <stdin>]

-o, --output FILENAME

Destination PFB file. [default: <stdout>]

Commands:

enum Rename enum. node Rename node. type Rename type (not implemented).

### Rename node

Usage: pfb rename [PARENT OPTIONS] node [OPTIONS] OLD NEW

Rename node from OLD to NEW.

### Rename enum

Usage: pfb rename [PARENT OPTIONS] enum [OPTIONS] FIELD OLD NEW

Rename enum of FIELD from OLD to NEW.

### Convert PFB into Neptune (bulk load format for Gremlin)

Usage: pfb to [PARENT OPTIONS] gremlin [OPTIONS] [OUTPUT]

Convert PFB into CSV files under OUTPUT for Neptune bulk load (Gremlin).

The default OUTPUT is ./gremlin/.

Options:

–gzip / –no-gzip Whether gzip the output. [default: yes]

## Examples

pfb from dict http://s3.amazonaws.com/dictionary-artifacts/kf-dictionary/1.1.0/schema.json > ./tests/schema/kf.avro

pfb from json ./tests/data -s ./tests/schema/kf.avro –program DEV –project test > tests/pfb-data/test.avro

cat tests/pfb-data/test.avro | pfb rename node slide slide_test > tests/pfb-data/rename_test.avro

cat tests/pfb-data/test.avro | pfb rename enum state validated validated_test > tests/pfb-data/rename_test.avro

cat tests/pfb-data/test.avro | pfb show -n 1 | jq

cat tests/pfb-data/test.avro | pfb show –schema | jq

cat tests/pfb-data/test.avro | pfb to gremlin ./output/

[1]: ./doc/metadata.svg