Export QC results to text files.

Script meant to be run by runner.sh, either directly
or via an intermediate script that consolidates all
the user outputs in one place.

bin/human_exports_qc.py

@@ -0,0 +1,89 @@
+#!/usr/bin/python3
+
+"""
+Export data that is entered directly into Dougal
+as opposed to being read from external sources.
+
+This data will be read back in when the database
+is recreated for an existing survey.
+"""
+
+import os
+from glob import glob
+import pathlib
+import string
+import configuration
+import preplots
+from datastore import Datastore
+
+def sane_name(filename):
+	allowed_chars = string.ascii_letters + string.digits + " _-#+&^%$!();:.,"
+	return ''.join([c for c in filename if c in allowed_chars])
+
+def write_file (filename, items):
+	filename.parent.mkdir(parents=True, exist_ok=True)
+	with open(filename, "w") as fd:
+		for item in items:
+			sequence = point = line = ""
+			if type(item["_id"]) == list:
+				if len(item["_id"]) == 2:
+					sequence, point = item["_id"]
+				elif len(item["_id"]) == 3:
+					sequence, point, line = item["_id"]
+			else:
+				sequence = item["_id"]
+
+			line = f"{sequence}\t{point}\t{line}\t{item['results']}\n"
+			fd.write(line)
+
+def qc_item(item, prefixes = [], index = None):
+	leader = "{:0>2d}".format(index) if index is not None else ""
+	name = sane_name(leader+" "+item["name"])
+	if "check" in item:
+		filename = pathlib.Path(*prefixes, name+".txt")
+		print("MKFILE", filename)
+		print("Export", len(item["check"]), "results")
+		write_file(filename, item["check"])
+
+	if "children" in item:
+		print("MKDIR", pathlib.Path(*prefixes, name))
+		subindex = 0
+		for child in item["children"]:
+			subindex += 1
+			qc_item(child, [*prefixes, name], subindex)
+
+def qc_data (cursor, prefix):
+	qc = db.get_info('qc', cursor)[0]
+	#print("QC", qc)
+	index = 0
+	for item in qc["results"]:
+		index += 1
+		qc_item(item, [prefix, "QC"], index)
+
+if __name__ == '__main__':
+
+	print("Reading configuration")
+	surveys = configuration.surveys()
+
+	print("Connecting to database")
+	db = Datastore()
+
+	print("Reading surveys")
+	for survey in surveys:
+		print(f'Survey: {survey["id"]} ({survey["schema"]})')
+		db.set_survey(survey["schema"])
+		with db.conn.cursor() as cursor:
+
+			try:
+				pathPrefix = survey["exports"]["human"]["path"]
+			except KeyError:
+				print("Survey does not define an export path for human data")
+				continue
+
+			if not pathlib.Path(pathPrefix).exists():
+				print(pathPrefix)
+				raise ValueError("Export path does not exist")
+
+			qc_data(cursor, pathPrefix)
+
+	print("Done")