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75 lines
2.1 KiB
Python
Executable File
75 lines
2.1 KiB
Python
Executable File
#!/usr/bin/python3
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"""
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Export data that is entered directly into Dougal
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as opposed to being read from external sources.
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This data will be read back in when the database
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is recreated for an existing survey.
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"""
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import os
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from glob import glob
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import pathlib
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import string
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import configuration
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import requests
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import json
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#from datastore import Datastore
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def sane_name(filename):
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allowed_chars = string.ascii_letters + string.digits + " _-#+&^%$!();:.,"
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return ''.join([c for c in filename if c in allowed_chars])
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def write_file (filename, payload):
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print("Writing to", filename)
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tmpname = filename.parent / (filename.name + ".tmp")
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filename.parent.mkdir(parents=True, exist_ok=True)
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with open(tmpname, "w", encoding="utf8") as fd:
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json.dump(payload, fd, indent=4, ensure_ascii=False)
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os.rename(tmpname, filename)
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def seis_data (survey):
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try:
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pathPrefix = survey["sse"]["path"]
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except KeyError:
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print("Survey does not define an export path for human data")
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return
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if not pathlib.Path(pathPrefix).exists():
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print(pathPrefix)
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raise ValueError("Export path does not exist")
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print(f"Requesting sequences for {survey['id']}")
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url = f"http://localhost:3000/api/project/{survey['id']}/sequence"
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r = requests.get(url)
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print(r.status_code, url)
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for sequence in r.json():
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if sequence['status'] not in ["final", "ntbp"]:
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continue
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filename = pathlib.Path(pathPrefix, "sequence{:0>3d}.json".format(sequence['sequence']))
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if filename.exists():
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print(f"Skipping export for sequence {sequence['sequence']} – file already exists")
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continue
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print(f"Processing sequence {sequence['sequence']}")
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url = f"http://localhost:3000/api/project/{survey['id']}/event?sequence={sequence['sequence']}&missing=t"
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headers = { "Accept": "application/vnd.seis+json" }
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r = requests.get(url, headers=headers)
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if r.status_code == requests.codes.ok:
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write_file(filename, r.json())
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if __name__ == '__main__':
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print("Reading configuration")
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surveys = configuration.surveys()
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print("Reading surveys")
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for survey in surveys:
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print(f'Survey: {survey["id"]} ({survey["schema"]})')
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seis_data(survey)
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print("Done")
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