def hide_some_files(collection, site):
# hide some files
hide_file = Query("HideFile")
for row in Query("FilesInCollectionSiteForSend").run(
collection=collection,
site=site):
count = hide_file.execute(row.file_id)
print(f"{row.file_id}: {count} row(s) updated")
def main():
get_import = Query("GetPosdaFilesImportControl")
go_in_service = Query("GoInServicePosdaImport")
quit_q = Query("RelinquishControlPosdaImport")
while True:
# get current status
for import_control in get_import.run(): pass
if import_control.status == "waiting to go inservice":
go_in_service.execute(MYPID)
continue
if import_control.status == "service process running":
if import_control.processor_pid != MYPID:
printe("Some other process controlling import")
return
if import_control.pending_change_request == "shutdown":
quit_q.execute()
printe("Relinquished control of posda_import")
return
printe("Doing actual work (well, pretending)")
else:
printe(f"unknown state ({import_control.status}) for posda_import")
def print_distinct_series_by_collsite(collection, site):
for row in Query("DistinctSeriesByCollectionSite").run(
site_name=site,
project_name=collection):
print(row)
break
else:
print(f"No collection/site {collection}//{site}")
def build_new_timepoint(activity_id, file_list: List[int]) -> None:
# Create the new timepoint
Query("CreateActivityTimepoint").execute(actiity_id=activity_id,
who_created='none',
comment='UncompressFilesTp.py',
creating_user='******')
tp_id = Query("GetActivityTimepointId").get_single_value()
with Database("posda_files").cursor() as cur:
# build a single giant insert query
args = b','.join(
[cur.mogrify("(%s, %s)", [tp_id, f]) for f in file_list])
query = b"""\
insert into activity_timepoint_file values
""" + args
cur.execute(query)
return tp_id
# from collections import namedtuple, defaultdict
help = """
Consume a posda filelist (plist) file and import all listed files into Posda.
"""
parser = args.Parser(arguments=[
args.CustomArgument("plist", "The Posda Filelist (plist) file to read"),
],
purpose="Import plist into posda",
help=help)
pargs = parser.parse()
# Preload queries that will be used in functions, so they aren't loaded repeatedly
get_posda_file_id_by_digest = Query("GetPosdaFileIdByDigest")
insert_file_posda = Query("InsertFilePosda")
get_current_posda_file_id = Query("GetCurrentPosdaFileId")
insert_file_import_long = Query("InsertFileImportLong")
make_posda_file_ready_to_process = Query("MakePosdaFileReadyToProcess")
insert_file_location = Query("InsertFileLocation")
get_matching_root = Query("GetMatchingRootID")
create_new_root = Query("InsertNewRootPath")
def make_rel_path_from_digest(digest):
return Path() / digest[:2] / digest[2:4] / digest[4:6] / digest
# def get_xfer_syntax(filename):
# try:
sop_seen_in_file[input_line.sop] += 1
print(f"Read {len(lines)} input lines.")
background.daemonize()
print(f"Comparing spreadsheet to Intake, for {pargs.collection}|{pargs.site}")
print(f"Read {len(lines)} input lines.")
sop_seen_in_query = defaultdict(int)
query = {}
Record = namedtuple("Record", ["patient_id", "sop_instance_uid", "study_instance_uid", "series_instance_uid"])
for row in Query("IntakeImagesByCollectionSitePlus").run(
collection=pargs.collection,
site=pargs.site):
decoded = [i.decode() for i in row]
row = Record(*decoded)
query[row.sop_instance_uid] = row
sop_seen_in_query[row.sop_instance_uid] += 1
Error = namedtuple("Error", ["sop", "type", "file_val", "intake_val"])
errors = []
def eq_or_err(sop, what, qval, lval):
if lval != qval:
errors.append(Error(sop, f"{what} mismatch", lval, qval))
for sop in lines:
if sop not in query:
_, invoc_id, activity_id, notify = sys.argv
# collect series from stdin
series = []
for line in sys.stdin:
series.append(line.strip())
series_count = len(series)
print(f"Going to background to process {series_count} series")
background = BackgroundProcess(invoc_id, notify, activity_id)
background.daemonize()
q = Query("SeriesInHierarchyBySeriesExtendedFurther")
start = time.time() # the epoch
# In python, after you call daemonize print will automatically
# print to the email
print("Initial line written to email")
hierarchy = None
report = background.create_report(f"DICOM Hierarchy for {series_count} series")
writer = csv.writer(report)
writer.writerow([
"collection",
"site",
"patient_id",
"study_instance_uid",
def main():
get_import = Query("GetPosdaFilesImportControl")
go_in_service = Query("GoInServicePosdaImport")
quit_q = Query("RelinquishControlPosdaImport")
while True:
# get current status
for import_control in get_import.run():
pass
if import_control.status == "waiting to go inservice":
go_in_service.execute(MYPID)
continue
if import_control.status == "service process running":
if import_control.processor_pid != MYPID:
printe("Some other process controlling import")
return
if import_control.pending_change_request == "shutdown":
quit_q.execute()
printe("Relinquished control of posda_import")
return
printe("Doing actual work (well, pretending)")
else:
printe(f"unknown state ({import_control.status}) for posda_import")
# site_name='MAASTRO',
# project_name='Radiomics') as r:
# for row in r:
# print(row)
# print(row.series_instance_uid)
# break
for row in Query("DistinctSeriesByCollectionSite").run(
site_name='MAASTRO',
project_name='Radiomics'):
print(row)
break
# hide some files
hide_file = Query("HideFile")
for row in Query("FilesInCollectionSiteForSend").run(
collection='Radiomics',
site='MAASTRO'):
count = hide_file.execute(row.file_id)
print(f"{row.file_id}: {count} row(s) updated")
# unhide all files
with Database("posda_files").cursor() as cur:
cur.execute("update ctp_file "
"set visibility = null "
"where visibility = 'hidden'")
# from collections import namedtuple, defaultdict
help = """
Consume a posda filelist (plist) file and import all listed files into Posda.
"""
parser = args.Parser(arguments=[
args.CustomArgument("plist", "The Posda Filelist (plist) file to read"),
],
purpose="Import plist into posda",
help=help)
pargs = parser.parse()
# Preload queries that will be used in functions, so they aren't loaded repeatedly
get_posda_file_id_by_digest = Query("GetPosdaFileIdByDigest")
insert_file_posda = Query("InsertFilePosda")
get_current_posda_file_id = Query("GetCurrentPosdaFileId")
insert_file_import_long = Query("InsertFileImportLong")
make_posda_file_ready_to_process = Query("MakePosdaFileReadyToProcess")
insert_file_location = Query("InsertFileLocation")
def make_rel_path_from_digest(digest):
return Path() / digest[:2] / digest[2:4] / digest[4:6] / digest
def get_xfer_syntax(filename):
try:
ds = pydicom.dcmread(filename)
return ds.file_meta.TransferSyntaxUID
args.Presets.description,
args.CustomArgument("file_query_name",
"Name of query to use for getting list of "
"files in given series"),
args.Presets.notify],
purpose="Background Process to scan for PHI",
help=help)
args = parser.parse()
# TODO: this (and some other stuff) could be moved into
# an util lib, posda.background.shortcuts or something?
subprocess_id = Query("CreateBackgroundSubprocess").get_single_value(
subprocess_invocation_id=args.background_id,
command_executed='???',
foreground_pid=os.getpid(),
user_to_notify=args.notify
)
if subprocess_id is None or subprocess_id == 0:
raise RuntimeError("Failed to get subprocess ID")
print(f"Subprocess_id is: {subprocess_id}")
input_lines = posda.main.get_stdin_input()
print(f"Found list of {len(input_lines)} series to scan")
print("Forking background process")
###############################################################################