pypfb 0.4.5

Python SDK for PFB format

# :construction: PFB Python SDK :construction:

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

## PyPFB Overview

PyPFB is a python sdk to create, explore, and modify PFB (Portable Format for Bioinformatics) files.

These files start from a Gen3 data dictionary. These can be made from either json hosted on a cloud storage service, like s3, or from a local directory. See PyPFB From Schema for an example.

Once we have a PFB file created from a schema we can start to add data to the file. This is done using JSON files from local directory. We create them in the style of our data-simulator https://github.com/uc-cdis/data-simulator/ Once we have them we can use PFB From JSON to import the structured json into our Serialized PFB file.

At this point we have a PFB file with married schema and serialized data. Now we have a few options for modifying these PFB files. These are good options for breaking changes within the dictionary. This allows a commons operator to export the entire structured database, make modifications to fix the breaking changes, and then re import the file back to the commons.

Changes that are already supported by this SDK are renames (enum and nodes) and adds of records data.

## 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 poetry install `

## 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.

Examples:

schema:

pfb show -i data.avro schema

nodes:

pfb show -i data.avro nodes

metadata:

pfb show -i data.avro metadata

records:

pfb show -i data.avro -n 5

### 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>]

Examples:

URL:

pfb from -o thing.avro dict https://s3.amazonaws.com/dictionary-artifacts/gtexdictionary/3.2.2/schema.json

Directory:

pfb from -o gdc.avro dict /path/to/dictionary/schemas/

### 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]

Example:

pfb from -o data.avro json -s schema.avro –program DEV –project test /path/to/data/json/

### 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>]

Example:

pfb make -i test.avro demographic > empty_demographic.json

### 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>]

Example:

pfb add -i new_record.json pfb.avro

### 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).

Examples:

enum:

pfb rename -i data.avro -o data_enum.avro enum demographic_ethnicity old_enum new_enum

node:

pfb rename -i data.avro -o data_update.avro node demographic information

### 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]

Example:

pfb to -i data.avro gremlin

### Example of minimal PFB

In the examples/minimal-pfb directory we have an example of a minimal pfb that only contains submitted unaligned read data

First create the PFB with schema from the json dictionary pfb from -o minimal_schema.avro dict minimal_file.json

Then we put the data into the PFB pfb from -o minimal_data.avro json -s minimal_schema.avro –program DEV –project test sample_file_json/

We can view the data of the PFB pfb show -i minimal_data.pfb

We can also view the schema of the PFB pfb show -i minimal_data.pfb schema

## 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/schema.svg