Export structured sequence data to JSON files.

Script meant to be run by runner.sh.

It will not overwrite existing files. If a
sequence is modified after the first export,
the resulting file needs to be removed by the
user before a re-export will occur.

The idea is to eventually export on demand
when a new raw is added to final_lines.

bin/human_exports_seis.py

@@ -0,0 +1,74 @@
+#!/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") as fd:
+		json.dump(payload, fd, indent=4)
+	os.rename(tmpname, filename)
+
+def seis_data (survey):
+	try:
+		pathPrefix = survey["exports"]["human"]["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, "SSE", "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']}"
+		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")