11a7d1aac16cfc653302a713b756fe4c352f450d max Mon May 19 02:34:40 2025 -0700 fixing panelApp bug, refs #35757 diff --git src/hg/utils/otto/panelApp/tandRep.py src/hg/utils/otto/panelApp/tandRep.py index b51584f63c0..003eee4b0a8 100644 --- src/hg/utils/otto/panelApp/tandRep.py +++ src/hg/utils/otto/panelApp/tandRep.py @@ -1,58 +1,34 @@ import requests import json import pandas as pd import sys import argparse import re +import cnv -def get_url(url): - page_count = 1 - jData = dict() - while True: - try: - new_url = "{}{}".format(url, page_count) - myResponse = requests.get(new_url) - if (myResponse.ok): - jData = json.loads(myResponse.content.decode()) - - # If jData is empty create, else append - if "error" in jData.keys(): - raise Exception("{} page count is missing.".format(page_count)) - else: - print('Json data retrieved') - break - except: - if page_count > 1: - print('Json data retrieved') - else: - print("Unable to request URL") - sys.exit() - break - print(page_count) - page_count += 1 - return jData - +from cnv import getAllPages def downloadTandReps(): Error = True continuous_count=0 - url = "https://panelapp.genomicsengland.co.uk/api/v1/strs/?page=" - jData = get_url(url) + url = "https://panelapp.genomicsengland.co.uk/api/v1/strs/?format=json" + res = getAllPages(url) - res = jData['results'] num_gene_data = len(res) + print("Got %d tandem repeats from API" % num_gene_data) + count = 0 continuous_count = 0 hg19_dict = dict() hg38_dict = dict() while count != num_gene_data: #if count == 10: # break string_dict_key = 'gene_{}'.format(continuous_count) temp_attribute_dictionary = dict() chromosome = res[count]['chromosome'] chromosome = 'chr{}'.format(chromosome) confidence_level = res[count]['confidence_level'] entity_name = res[count]['entity_name']