Avantol13’s gists

Avantol13 / openapi.yaml

Created February 4, 2021 18:35

	components:
	schemas:
	AggregatedResponses:
	properties:
	commonsA:
	type: object
	$ref: '#/components/schemas/AggregatedResponse'
	commonsB:
	type: object
	$ref: '#/components/schemas/AggregatedResponse'

Avantol13 / bdc_discovery_data_extract.py

Last active March 1, 2021 16:53

	"""
	Script to get initial metadata for BDCat studies from Gen3 Graph and by scraping dbGaP.

	Available tags:

	Program
	- TOPMed
	- COVID 19

	Study Registration

Avantol13 / add_access_datasets.py

Last active October 16, 2020 20:59

	"""
	Populate ACCESS User Management System with Datasets
	Also generate commands for linking Gen3 Google Groups based on mapping file provided

	* You need gen3 package so `pip install gen3`
	* Download TSV of current production ACCESS list after logging in as Super Admin
	* `generate_ACCESS_info` in `generate.py` to output a new `ACCESS_info.txt`
	* A list of new/updated studies in the format like:
	* phs_consent, authid, full_name
	* Log into the commons, download an API key and set the filepath API_KEY_FILEPATH

Avantol13 / metadata_manifest_qa.py

Created October 5, 2020 18:58

	import argparse
	import os
	import sys
	import sys
	import logging
	import asyncio

	from gen3.tools import metadata

	# TODO: Maybe this script to its own repo to be distributed properly

Avantol13 / export_eps.py

Created August 30, 2020 16:54

	#!/usr/bin/env python

	from gimpfu import *

	# can run in python console with default values with:
	# pdb.python_fu_export_eps("", "test23.eps", 0, 0)

	def export_eps(folder, filename, width, height):
	folder = folder or "F:\\_GoogleDrive\\Other Projects\\Board Games\\Food Game\\_cards"
	width = width or 699.1

Avantol13 / ga4gh_dbgap_passport_ex2.json

Last active June 19, 2020 17:40

	{
	"ga4gh_passport_v1":
	[
	{
	"iss": "https://stsstg.nih.gov",
	"sub": "Ei4sFoHQ1KO-foobar",
	"iat": 1588686798,
	"exp": 1588729998,
	"scope": "email profile ga4gh_passport_v1 openid",
	"jti": "42d1e574-4129-4ee1-8a07-fa6a8d8bffcf",

Avantol13 / ga4gh_dbgap_passport_ex.json

Last active June 19, 2020 17:40

	{
	"ga4gh_passport_v1":
	[
	{
	"iss": "https://stsstg.nih.gov",
	"sub": "Ei4sFoHQ1KO-foobar",
	"iat": 1588686798,
	"exp": 1588729998,
	"scope": "email profile ga4gh_passport_v1 openid",
	"jti": "42d1e574-4129-4ee1-8a07-fa6a8d8bffcf",

Avantol13 / test_indexing.tsv

Last active May 18, 2020 21:25

	guid	md5	size	acl	authz	urls
	c519fedb-686a-4b96-b910-65355d3ea0ab	f0aa6ed73a82379a6b8150a3e2b2b42c	12345678345	phs000964.c1 admin	/programs/DEV	gs://topmed-irc-share/test2

Avantol13 / public_indexing_manifest.csv

Created April 9, 2020 20:41

We can't make this file beautiful and searchable because it's too large.

	guid,urls,authz,acl,md5,file_size,file_name
	2e4f042b-55fd-481a-ae6c-5102357bafe4,gs://dcf-integration-test/NWD437822.txt s3://cdis-presigned-url-test/testdata,/programs/DEV/projects/test,,f0aa6ed73a82379a6b8150a3e2b2b42c,42,
	c65ae178-e070-4a33-a091-bca0516b6ab3,s3://cdis-presigned-url-test/NWD680715 gs://dcf-integration-test/file.txt,/programs/DEV/projects/test,,443e7594cbe3275a152906392e433e8d,42,
	b81501c5-034c-415a-9a28-989296e9e5b2,s3://cdis-presigned-url-test/testdata gs://dcf-integration-test/file.txt,/programs/DEV/projects/test,,5c4395d5062ae6235a8b8b91752a5a75,42,
	5a030535-3257-4b7a-93cd-b60934e711c3,s3://cdis-presigned-url-test/testdata gs://dcf-integration-test/file.txt,/programs/DEV/projects/test,,7edd57cdc3405c9e94909e59da55405b,42,
	092b8c05-c848-4397-8884-38bdb9e0b00f,s3://cdis-presigned-url-test/testdata gs://dcf-integration-test/file.txt,/programs/DEV/projects/test,,d873dcebf8c7056a2aede0e588e3b9bd,42,

Avantol13 / public_dbgap_metadata_manifest.tsv

Last active April 10, 2020 15:58

We can make this file beautiful and searchable if this error is corrected: Unclosed quoted field in line 3.

	guid submitted_sample_id biosample_id dbgap_sample_id sra_sample_id submitted_subject_id dbgap_subject_id consent_code consent_short_name sex body_site analyte_type sample_use repository dbgap_status sra_data_details study_accession study_accession_with_consent study_with_consent study_subject_id
	c65ae178-e070-4a33-a091-bca0516b6ab3 NWD680715 SAMN04109058 1784155 SRS1361261 DBG00391 1360750 2 HMB-IRB-MDS female Blood DNA "[""Seq_DNA_SNP_CNV"", ""WGS""]" TOPMed_WGS_Amish Loaded "{""status"": ""public"", ""experiments"": ""1"", ""runs"": ""1"", ""bases"": ""135458977924"", ""size_Gb"": ""25"", ""experiment_type"": ""WGS"", ""platform"": ""ILLUMINA"", ""center"": ""UM-TOPMed""}" phs000956.v4.p1 phs000956.v4.p1.c2 phs000956.c2 phs000956.v4_DBG00391
	2e4f042b-55fd-481a-ae6c-5102357bafe4 NWD437822 SAMN11169121 3415113 SRS4907945 BUR02263239B 2199582 2 DS-LD-IRB-COL male Peripheral Blood DNA "[""Seq_DNA_SNP_CNV"", ""WGS""]" GALAII Loaded "{""status"": ""public"", ""experiments"": ""1"", ""runs"": ""1"", ""bases"": ""

Alexander VanTol Avantol13