dougal-software/bin/human_exports_seis.py

#!/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 requests
import json
#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, payload):
	print("Writing to", filename)
	tmpname = filename.parent / (filename.name + ".tmp")
	filename.parent.mkdir(parents=True, exist_ok=True)
	with open(tmpname, "w", encoding="utf8") as fd:
		json.dump(payload, fd, indent=4, ensure_ascii=False)
	os.rename(tmpname, filename)

def seis_data (survey):
	try:
		pathPrefix = survey["sse"]["path"]
	except KeyError:
		print("Survey does not define an export path for human data")
		return

	if not pathlib.Path(pathPrefix).exists():
		print(pathPrefix)
		raise ValueError("Export path does not exist")

	print(f"Requesting sequences for {survey['id']}")
	url = f"http://localhost:3000/api/project/{survey['id']}/sequence"
	r = requests.get(url)
	print(r.status_code, url)
	for sequence in r.json():
		if sequence['status'] not in ["final", "ntbp"]:
			continue

		filename = pathlib.Path(pathPrefix, "sequence{:0>3d}.json".format(sequence['sequence']))
		if filename.exists():
			print(f"Skipping export for sequence {sequence['sequence']} – file already exists")
			continue

		print(f"Processing sequence {sequence['sequence']}")
		url = f"http://localhost:3000/api/project/{survey['id']}/event?sequence={sequence['sequence']}&missing=t"
		headers = { "Accept": "application/vnd.seis+json" }
		r = requests.get(url, headers=headers)
		if r.status_code == requests.codes.ok:
			write_file(filename, r.json())


if __name__ == '__main__':

	print("Reading configuration")
	surveys = configuration.surveys()

	print("Reading surveys")
	for survey in surveys:
		print(f'Survey: {survey["id"]} ({survey["schema"]})')
		seis_data(survey)

	print("Done")