biostream/bioschemas

Name: bioschemas

Owner: biostream

Description: ga4gh, gdc and bmeg in one place

Created: 2016-11-11 21:37:22.0

Updated: 2017-09-08 20:58:29.0

Pushed: 2017-07-14 22:03:15.0

Homepage:

Size: 129

Language: Protocol Buffer

GitHub Committers

User	Most Recent Commit	# Commits
Brian	2017-04-19 16:58:44.0	12
Kyle Ellrott	2017-03-28 19:02:07.0	2
Brian King	2017-01-06 21:53:31.0	12

Other Committers

User	Email	Most Recent Commit	# Commits

README

bioschemas

Common data structures and APIs.

This repo contains

• git submodules from ga4gh, gdc and bmeg
• A utility to read the schemas and produce different output (jsonschema and cerberus)

packaging

The schemas are packaged into a python module bioschemas The justification for the packaging is threefold:

• Moves complexities of gitmodule management from the end user to the package release process
• Each of the submodules referenced have many other components other than the schemas themselves. Packaging allows us to trim all components other than schema source.
• The generated snapshot is checked into git - the rationalization is that is allows us to tag package explicitly and allows clients to install the package without submodule complexity.

install git+https://github.com/ohsu-computational-biology/bioschemas

package release

in
ckage-all.sh
 generates schema snapshot ...
 runs setup tests ...
------------------------------------------------------------------
4 tests in 0.100s

usage

oschemas-snapshot --help
e: bioschemas-snapshot [-h] [-o OUTPUT] [-v]

act bioschemas schema directory [ga4gh,bmeg,gdc]

onal arguments:
, --help            show this help message and exit
 OUTPUT, --output OUTPUT
                    Extract to this directory name. Must not already
                    exist; it will be created as well as missing parent
                    directories.
, --version         Print git hashes

The snapshot can be used by any language context and has the following structure:

cerberus
??? bmeg
??? ga4gh
?   ??? ga4gh
?   ??? google
?       ??? api
?       ??? protobuf
??? gdc
jsonschema
??? bmeg
??? ga4gh
?   ??? ga4gh
?   ??? google
?       ??? api
?       ??? protobuf
??? gdc
proto
??? bmeg
??? ga4gh
    ??? ga4gh
    ??? google
        ??? api

python usage

rt  bioschemas

chemas.schema_path()
/home/someuser/bioschemas/bioschemas/snapshot'

schemas.json_schema('Resource')
u'properties': {u'checksum': {u'type': u'string'}, u'class': {u'type': u'string'}, u'created': {u'type': u'string'}, u'datasetID': {u'type': u'string'}, u'description': {u'type': u'string'}, u'format': {u'type': u'string'}, u'gid': {u'type': u'string'}, u'id': {u'type': u'string'}, u'info': {u'type': u'object'}, u'location': {u'type': u'string'}, u'mimeType': {u'type': u'string'}, u'name': {u'type': u'string'}, u'size': {u'type': u'integer'}, u'type': {u'type': u'string'}}, u'type': u'object'}  

schemas.cerberus_schema('Resource')
u'checksum': {u'type': u'string'}, u'class': {u'type': u'string'}, u'created': {u'type': u'string'}, u'datasetID': {u'type': u'string'}, u'description': {u'type': u'string'}, u'format': {u'type': u'string'}, u'gid': {u'type': u'string'}, u'id': {u'type': u'string'}, u'info': {u'type': {u'type': u'dict'}}, u'location': {u'type': u'string'}, u'mimeType': {u'type': u'string'}, u'name': {u'type': u'string'}, u'size': {u'type': u'integer'}, u'type': {u'type': u'string'}}

chemas.git_hashes()
{u'bioschemas': u'f40f653', u'bmeg': u'537f94a', u'created_at': u'2016-11-18T17:47:56.858397Z', u'gdc': u'288f042'}

chemas.gdc_submission_template('file')

u'aliquots': {u'submitter_id': None}, u'analytes': {u'submitter_id': None}, u'archives': {u'submitter_id': None}, u'cases': {u'submitter_id': None}, u'centers': {u'code': None}, u'data_formats': {u'name': None}, u'data_subtypes': {u'name': None}, u'derived_files': {u'submitter_id': None}, u'described_cases': {u'submitter_id': None}, u'experimental_strategies': {u'name': None}, u'file_name': None, u'file_size': None, u'md5sum': None, u'platforms': {u'name': None}, u'portions': {u'submitter_id': None}, u'project_id': None, u'related_files': {u'submitter_id': None}, u'samples': {u'submitter_id': None}, u'slides': {u'submitter_id': None}, u'state_comment': None, u'submitter_id': None, u'tags': {u'name': None}, u'type': u'file'}

utilty

The ga4gh and bmeg cannonical schemas are maintained in protobuf. The bin/custom-plugin.py processes the schemas for alternate uses (jsonschema, cerebus). The bioschemas/snapshot directory contains output from protoc. Please do not hand edit, rather change custom-plugin.py or json-to-cerberus.py