Avantol13’s gists

Avantol13 / .bashrc

Created April 4, 2018 16:01

	# other stuff ...

	# open git cola (https://git-cola.github.io/) easier
	alias gc='git-cola &'

	# enter friendly interactive shell easier (https://fishshell.com/)
	alias f='fish'

	# create and checkout new branch easier, stash stuff before if needed
	gitbranch(){

Avantol13 / nested_dict_replace.py

Last active June 13, 2018 22:53

Replace nested value in dict from another nested value in a different dict

	import copy

	def replace(data, path_to_key, replacement_value):
	"""
	Will replace a nested value in a dict with the given value.
	Args:
	data (dict): a dictionary
	path_to_key (str): nested/path/to/key. The value of this key will be
	replaced
	replacement_value (str): Replacement value for the key from

Avantol13 / g_sign.py

Created September 28, 2018 14:28

generating signed url for requester pays bucket, bill to project that owns the bucket

	# NOTE: need to install oauth2client
	# Signed URL generates correctly but I keep getting:
	# <Error>
	# <Code>SignatureDoesNotMatch</Code>
	# <Message>
	# The request signature we calculated does not match the signature you provided. Check your Google secret key and signing method.
	# </Message>
	# ...
	# </Error>

Avantol13 / dictionaries_match.py

Created October 24, 2018 15:40

Check if two dictionaries in Python have the same key structure/schema


	def dictionaries_match(d1, d2):
	# both are dicts, need to check values
	if isinstance(d1, dict) and isinstance(d2, dict):
	d1_keys = d1.keys()
	d1_keys.sort()
	d2_keys = d2.keys()
	d2_keys.sort()
	valid = d1_keys == d2_keys and all(
	dictionaries_match(d1[k], d2[k]) for k in d1.keys()

Avantol13 / mock_file.py

Created November 30, 2018 22:24

	# Python 2
	from mock import patch, mock_open

	creds_file = "This text is not really in a file."
	mocked_open = patch("__builtin__.open", mock_open(read_data=creds_file))
	mocked_open.start()

	with open("any_file_name") as mocked_file:
	print(mocked_file.read())

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"": ""

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,
	85b9605f-e92d-4020-8caa-290ca6aeb09c,gs://dcf-integration-test/file.txt s3://cdis-presigned-ur

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 / 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 / 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",

Alexander VanTol Avantol13