import shutil
import tempfile
import subprocess
from posda.queries import Query
from posda.main import args
from posda.util import md5sum
# 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")
from posda.main import args
import os
import sys
import csv
from multiprocessing import Pool, Queue
help = """
Build a spreadsheet report from a directory.
This script does not read from stdin.
"""
parser = args.Parser(arguments=[
args.Presets.background_id,
args.CustomArgument("scan_dir", "The directory to build the report from"),
args.Presets.notify
],
purpose="Build a report from a directory",
help=help)
pargs = parser.parse()
print(f"Building report for dir: {pargs.scan_dir}")
print(f"This script does not read lines from stdin, so no lines read")
background = BackgroundProcess(pargs.background_id, pargs.notify)
background.daemonize()
background.log_input_count(0)
A report is generated which compares each image, matching on SOP Instance UID.
Input is read from STDIN. Lines should be in the form:
<filename>,<collection>,<site>,<patient>,<series>,<sop>,<md5sum>,<size>
(basically CSV)
An output report will be generated and emailed to NOTIFY, and will contain
details of the following discrepencies:
* SOPs missing from the file, or in Intake
* Duplicate SOP entires in file, or in Intake
* Data mismatch in Patient ID/Series Instance UID
"""
parser = args.Parser(
arguments=[args.Presets.background_id,
args.CustomArgument("collection",
"The collection to compare against"),
args.CustomArgument("site",
"The site to compare against"),
args.Presets.notify],
purpose="Compare a spreadsheet report to Intake",
help=help)
pargs = parser.parse()
background = BackgroundProcess(pargs.background_id, pargs.notify)
reader = csv.reader(sys.stdin)
lines = {}
header = 'filename,collection,site,patient,series,sop,md5sum,size'.split(',')
InputLine = namedtuple("InputLine", header)
help = """
Runs a scan for PHI.
file_query_name can be one of:
"IntakeFilesInSeries" - get list of series in intake database
"PublicFilesInSeries" - get list of series in public database
"FilesInSeries" - get list of series in posda database
Expects a list of series on STDIN
"""
parser = args.Parser(
arguments=[args.Presets.background_id,
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