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#!/usr/bin/env python3 |
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# -*- coding: utf-8 -*- |
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""" |
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Created on Wed Mar 27 12:50:16 2019 |
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@author: Paolo Cozzi <[email protected]> |
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""" |
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import re |
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import logging |
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import datetime |
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import websockets |
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import time |
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import json |
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from dateutil.relativedelta import relativedelta |
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from django.conf import settings |
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from django.contrib.admin.utils import NestedObjects |
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from django.db import DEFAULT_DB_ALIAS |
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from django.utils.text import capfirst |
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from django.utils.encoding import force_text |
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from .constants import YEARS, MONTHS, DAYS, OBO_URL, TIME_UNITS |
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# Get an instance of a logger |
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logger = logging.getLogger(__name__) |
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def image_timedelta(t1, t2): |
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"""A function to deal with image time intervals. Returns a number and |
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time unit""" |
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if t1 is None or t2 is None: |
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logger.warning("One date is NULL ({0}, {1}) ignoring".format(t2, t1)) |
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return None, YEARS |
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if t2 > t1: |
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logger.warning("t2>t1 ({0}, {1}) ignoring".format(t2, t1)) |
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return None, YEARS |
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# check for meaningful intervald |
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if t1.year == 1900 or t2.year == 1900: |
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logger.warning("Ignoring one date ({0}, {1})".format(t2, t1)) |
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return None, YEARS |
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rdelta = relativedelta(t1, t2) |
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if rdelta.years != 0: |
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return rdelta.years, YEARS |
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elif rdelta.months != 0: |
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return rdelta.months, MONTHS |
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else: |
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return rdelta.days, DAYS |
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PATTERN_INTERVAL = re.compile(r"([\d]+) ([\w]+s?)") |
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def parse_image_timedelta(interval): |
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"""A function to parse from a image_timdelta string""" |
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match = re.search(PATTERN_INTERVAL, interval) |
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# get parsed data |
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value, units = match.groups() |
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# time units are plural in database |
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if units[-1] != 's': |
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units += 's' |
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# get time units from database |
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units = TIME_UNITS.get_value_by_desc(units) |
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return int(value), units |
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# https://stackoverflow.com/a/39533619/4385116 |
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# inspired django.contrib.admin.utils.get_deleted_objects, this function |
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# tries to determine all related objects starting from a provied one |
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# HINT: similar function at https://gist.github.com/nealtodd/4594575 |
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def get_deleted_objects(objs, db_alias=DEFAULT_DB_ALIAS): |
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# NestedObjects is an imporovement of django.db.models.deletion.Collector |
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collector = NestedObjects(using=db_alias) |
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collector.collect(objs) |
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def format_callback(obj): |
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opts = obj._meta |
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no_edit_link = '%s: %s' % (capfirst(opts.verbose_name), |
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force_text(obj)) |
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return no_edit_link |
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to_delete = collector.nested(format_callback) |
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protected = [format_callback(obj) for obj in collector.protected] |
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model_count = { |
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model._meta.verbose_name_plural: |
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len(objs) for model, objs in collector.model_objs.items()} |
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return to_delete, model_count, protected |
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async def send_message_to_websocket(message, pk): |
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""" |
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Function will create websocket object and send message to django-channels |
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Args: |
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message (dict): message to send to websocket |
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pk (str): primary key of submission |
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""" |
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# Need to have it here as in case with small test data message sent to |
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# websocket will overcome response from server |
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time.sleep(3) |
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async with websockets.connect( |
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'ws://asgi:8001/image/ws/submissions/{}/'.format(pk)) as websocket: |
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await websocket.send(json.dumps(message)) |
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def format_attribute(value, terms=None, library_uri=OBO_URL, units=None): |
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"""Format a generic attribute into biosample dictionary""" |
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if value is None: |
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return None |
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# pay attention to datetime objects |
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if isinstance(value, datetime.date): |
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value = str(value) |
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# HINT: need I deal with multiple values? |
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result = {} |
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result["value"] = value |
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if terms: |
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result["terms"] = [{ |
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"url": "/".join([ |
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library_uri, |
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terms]) |
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}] |
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if units: |
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result["units"] = units |
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# return a list of dictionaries |
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return [result] |
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def get_admin_emails(): |
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"""Return admin email from image.settings""" |
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ADMINS = settings.ADMINS |
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# return all admin mail addresses |
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return [admin[1] for admin in ADMINS] |
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def uid2biosample(value): |
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"""Convert human-readable name to model field""" |
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if value == 'Sample storage': |
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return 'storage' |
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elif value == 'Sample storage processing': |
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return 'storage_processing' |
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elif value == 'Sampling to preparation interval': |
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return 'preparation_interval_units' |
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return '_'.join(value.lower().split(" ")) |
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cnr-ibba /
IMAGE-InjectTool
