James Stevenson jsstevenson

dgidb-example

2023-12-15

Querying DGIdb GraphQL API

Load packages:

library("ghql")

VICC Normalizer DB Setup

Wagner Lab 2021

Prerequisites

A Python 3 installation
Pipenv
Java (probably at least version 8)

Pipenv introduction

Wagner Lab 2021

Purpose

Pipenv is a wrapper around Python's package installation and virtual environment utilities, allowing for us to specify dependencies in a consistent and reproducible manner. It creates a virtual Python executable and enables you to install external libraries without creating version conflicts in your other projects.

	[ issue-132-tests ⚙ venv] ~/code/fusor % ipython
	Python 3.11.0 (main, Sep 6 2023, 12:48:52) [Clang 14.0.3 (clang-1403.0.22.14.1)]
	Type 'copyright', 'credits' or 'license' for more information
	IPython 8.16.1 -- An enhanced Interactive Python. Type '?' for help.

	In [1]: from gene.database import create_db

	In [2]: db = create_db()

	In [3]: db.get_source_metadata("NCBI")

	(gene-normalization) ~/code/gene-normalization (issue-112) % ipython
	Python 3.9.12 (main, Mar 26 2022, 15:51:15)
	Type 'copyright', 'credits' or 'license' for more information
	IPython 8.2.0 -- An enhanced Interactive Python. Type '?' for help.

	In [2]: import boto3

	In [3]: g = boto3.resource("dynamodb").Table("gene_concepts")

	In [4]: from boto3.dynamodb.conditions import Key

	//
	// top level qs:
	// * any Array-style components require members?
	// * any scalar-style components require values? (ie can be Optional?)
	const example = {
	// ** reading frame preserved
	// mandatory?
	// how to (if needed?) represent 'unknown'?
	// not required to be included -- fusor // null
	// curation tool -- should be yes or no

	{
	"r_frame_preserved": true,
	"domains": [
	{
	"status": "preserved",
	"name": "tyrosine kinase catalytic domain",
	"id": "<computed>",
	"coordinates": "{<computed>}",
	"gene": {
	"symbol": "NTRK1",

	{
	"query": "rxcui:2555",
	"warnings": null,
	"match_type": 100,
	"value_object_descriptor": {
	"id": "normalize.therapy:rxcui%3A2555",
	"type": "TherapyDescriptor",
	"value": {
	"type": "Therapy",
	"id": "rxcui:2555"

	('ncbigene:100131223', {'src_name': 'NCBI', 'concept_id': 'ncbigene:100131223', 'symbol': 'LOC100131223', 'strand': '-', 'locations': [{'type': <VRSTypes.SEQUENCE_LOCATION: 'SequenceLocation'>, 'start': 28120833, 'end': 28121467, 'sequence_id': 'ga4gh:SQ.Ya6Rs7DHhDeg7YaOSg1EoNi3U_nQ9SvO'}], 'label_and_type': 'ncbigene:100131223##identity', 'item_type': 'identity'})
	('ncbigene:440585', {'src_name': 'NCBI', 'xrefs': ['hgnc:34347'], 'concept_id': 'ncbigene:440585', 'symbol': 'FAM183A', 'strand': '+', 'locations': [{'type': <VRSTypes.SEQUENCE_LOCATION: 'SequenceLocation'>, 'start': 43142961, 'end': 43156396, 'sequence_id': 'ga4gh:SQ.Ya6Rs7DHhDeg7YaOSg1EoNi3U_nQ9SvO'}], 'label_and_type': 'ncbigene:440585##identity', 'item_type': 'identity'})
	('ncbigene:51668', {'src_name': 'NCBI', 'xrefs': ['hgnc:25019'], 'concept_id': 'ncbigene:51668', 'symbol': 'HSPB11', 'strand': '-', 'locations': [{'type': <VRSTypes.SEQUENCE_LOCATION: 'SequenceLocation'>, 'start': 53911575, 'end': 53946305, 'sequence_id': 'ga4gh:SQ.Ya6Rs7DHhDe