def merge_pacs_ris(pacs):
""" Insert ris report into converted pacs json file"""
config = load_config()
uses_basis_auth = bool(config["REPORT_USES_BASIC_AUTH"])
use_reports = bool(config["REPORT_USE"])
user = config["REPORT_USER"]
pwd = config["REPORT_PWD"]
my_dict = []
print(f"Getting RisReport for {len(pacs)} studies")
for entry in pacs:
dic = {}
dic = entry.copy()
if not use_reports:
dic["RisReport"] = ""
my_dict.append(dic)
elif "AccessionNumber" in entry:
aNum = str(entry["AccessionNumber"])
url = get_report_show_url(config) + aNum + "&output=text"
if uses_basis_auth:
response = get(url, auth=HTTPBasicAuth(user, pwd))
else:
response = get(url)
response.raise_for_status()
data = response.text
dic["RisReport"] = data
my_dict.append(dic)
return my_dict
def run(self):
config = load_config()
results = query_study_description(
config, self.study_description, self.from_date, self.to_date
)
with self.output().open('w') as outfile:
w.write_file(results, outfile)
def requires(self):
config = load_config()
results = query_day_accs(config, self.day)
logging.debug(
f"Got {len(results)} accession number for day: {self.day}")
for i in results:
if "AccessionNumber" in i:
yield DailyUpConvertedMerged({"acc": i["AccessionNumber"]})
def run(self):
config = load_config()
study_uids = []
with self.input().open("r") as f:
for line in f:
study_uids.append(line.strip())
results = []
for study_uid in study_uids:
results.append(query_accession_number(config, study_uid))
flat = [item for sublist in results for item in sublist]
with self.output().open("w") as outfile:
w.write_file(flat, outfile)
def run(self):
config = load_config()
upload_url = get_solr_upload_url(config)
logging.debug("Uploading to url %s", upload_url)
with self.input().open("r") as in_file:
file = {"file": (in_file.name, in_file, "application/json")}
update_response = requests.post(
url=upload_url, files=file, params={"commit": "true"}
)
if not update_response.ok:
update_response.raise_for_status()
else:
with self.output().open("w") as my_file:
my_file.write("Upload successful")
def run(self):
config = load_config()
post_url = config.get("CDWH_STORE_URL", "")
if not post_url:
print(
"No CDWH_STORE_ULR configured in instance/config.cfg, exiting."
)
exit(1)
with self.input().open("r") as daily:
json_in = json.load(daily)
r = requests.post(post_url, json=json_in)
r.raise_for_status()
with self.output().open("w") as o:
o.write("done")