251 lines
11 KiB
Python
251 lines
11 KiB
Python
import csv
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import json
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import re
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from os.path import isfile
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from app.models import *
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from app.formats import *
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from django.db import transaction
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# Correct commas inside of a linked field
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def fix_bracketed_lists(data):
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for fix in re.findall(r'\([^\s]*,[ ]*[^\s]*\)', data):
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data = data.replace(fix, fix.replace(',', ' /'))
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return data
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# Check for valid link
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def fix_url(link):
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if len(link) > 3 and not link.startswith('http'):
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link = 'http://' + link
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# link = link.split(';')[0]
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return link
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# Create linked objects
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def add_linked(person, obj, data):
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field = []
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# TODO: fuzzy matching instead of lower()
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items = fix_bracketed_lists(data).lower()
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items = items.replace(';', ',').split(',')
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for i in items:
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n = i.strip()
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if len(n) < 3:
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continue
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tgt = obj.objects.filter(name=n).first()
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if not tgt:
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tgt = obj()
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tgt.name = n
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tgt.save()
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field.append(tgt)
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return field
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# Fetch an object by source_id (numeric identifier used in source DB)
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def get_by_id(rowid, obj, first=True):
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if type(rowid) is str and rowid.isdigit():
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rowid = int(rowid)
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if type(rowid) is int:
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l = obj.objects.filter(source_id=rowid)
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if first:
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return l.first(), rowid
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else:
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return l, rowid
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return None, None
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# Quick check of the number of lines
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def get_total_rows_csv(filename):
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with open(filename) as f:
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for i, l in enumerate(f):
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pass
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return i + 1
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# Search index routine
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def reindex_data():
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for i, p in enumerate(Person.objects.all()):
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p.index()
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p.save()
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# Data update routine
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def refresh_data(filename, fmt=None, update_existing=False):
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print("refresh_data")
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count = 0
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rowcount = 0
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if not isfile(filename):
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msg = "Missing data: %s - refresh aborted." % fmt['filename']
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print(msg)
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yield msg, "error"
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return None
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if fmt['extension'] == 'csv':
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totalrows = get_total_rows_csv(filename)
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with open(filename, 'rt', encoding='utf-8', errors='ignore') as csvfile:
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datareader = csv.DictReader(csvfile)
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for row in datareader:
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rowcount += 1
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if row is None:
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continue
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yield rowcount, rowcount / totalrows
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# # Ensure any new data is flushed from time to time
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# if count % 25 == 0:
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# db.session.commit()
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for r in fmt['required']:
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if not r in row:
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msg = "Missing attribute in %s (%s)" % (r, fmt['filename'])
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print(msg)
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yield msg, "error"
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return None
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if fmt['dataformat'] is DataFormat.PERSON_DETAIL:
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print(row)
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person, source_id = get_by_id(row['ID'], Person)
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if not person:
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person = Person.objects.filter(first_name=row['First name'], last_name=row['Last name']).first()
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if person:
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print("Fetched from DB")
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else:
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print("Does not exist in DB")
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if not person:
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person = Person(first_name=row['First name'], last_name=row['Last name'], source_id=row['ID'])
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person.source_id = source_id
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person.title = row['Title']
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print(row)
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person.organisation = row['Organisation English']
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print("Country = %s" % row['country'] if 'country' in row else '')
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if 'country' not in row or row['country'] is None or row['country'].strip() == '':
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row['country'] = 0
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c = Country.objects.get(id=row['country'])
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person.country = c
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person.position = row['Position']
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person.biography = row['Biography']
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person.contact_email = row['e-mail 1']
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person.personal_url = fix_url(row['URL'])
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person.save()
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print("Created")
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# Update data fields
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if update_existing:
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person.source_id = source_id
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person.title = row['Title']
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print(row)
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person.organisation = row['Organisation English']
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print("Country = %s" % row['country'] if 'country' in row else '')
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if 'country' not in row or row['country'] is None or row['country'].strip() == '':
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row['country'] = 0
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c = Country.objects.get(id=row['country'])
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person.country = c
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person.position = row['Position']
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person.biography = row['Biography']
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person.contact_email = row['e-mail 1']
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person.personal_url = fix_url(row['URL'])
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person.save()
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with transaction.atomic():
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research_methods = add_linked(person, Method, row['Methods'])
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methods_people = [MethodsPeople.objects.get_or_create(method_id=m.id, person_id=person.id)[0] for m in research_methods]
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person.methodspeople_set.set(methods_people)
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research_scales = add_linked(person, Scale, row['Scale'])
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scales_people = [ScalesPeople.objects.get_or_create(scale_id=s.id, person_id=person.id)[0] for s in research_scales]
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person.scalespeople_set.set(scales_people)
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research_taxa = add_linked(person, Taxon, row['Taxa'])
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taxa_people = [TaxaPeople.objects.get_or_create(taxon_id=t.id, person_id=person.id)[0] for t in research_taxa]
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person.taxapeople_set.set(taxa_people)
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research_fields = add_linked(person, Field, row['Field of expertise'])
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fields_people = [FieldsPeople.objects.get_or_create(field_id=f.id, person_id=person.id)[0] for f in research_fields]
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person.fieldspeople_set.set(fields_people)
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# research_ranges = add_linked(person, MountainRange, row['MountainRange'])
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# ranges_people = [RangesPeople.objects.get_or_create(range_id=r.id, person_id=person.id)[0] for r in research_ranges]
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# person.rangespeople_set.set(ranges_people)
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person.index()
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person.save()
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count = count + 1
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elif fmt['dataformat'] is DataFormat.RESOURCE_DETAIL:
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res, source_id = get_by_id(row['ID'], Resource)
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if not res:
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res = Resource(source_id=source_id)
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res.title = row['Title']
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res.citation = row['Citation']
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res.url = fix_url(row['URL'].strip('#')) # remove weird #formatting#
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res.abstract = row['Abstract']
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res.save()
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count = count + 1
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elif fmt['dataformat'] is DataFormat.RANGE_DETAIL:
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rng, source_id = get_by_id(row['Range_ID'], MountainRange)
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if not rng: rng = MountainRange(source_id=source_id)
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rng.gmba_id = row['GMBA_ID']
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rng.name = row['RangeName']
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rng.countries = row['Countries']
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rng.save()
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count = count + 1
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elif fmt['dataformat'] is DataFormat.PERSON_RESOURCE:
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rzs, source_id = get_by_id(row['Resource'], Resource, first=False)
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if not rzs or not rzs.first():
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continue
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ppl, source_id = get_by_id(row['Person'], Person, first=False)
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if not ppl or not ppl.first():
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continue
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for person in ppl:
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person.resources = []
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for r in rzs:
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person.resources.append(r)
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person.save()
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count = count + 1
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elif fmt['dataformat'] is DataFormat.PERSON_RANGE:
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rzs, source_id = get_by_id(row['MountainRange'], MountainRange, first=False)
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print(" range=%s, source_id=%s" % (rzs, source_id))
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if not rzs or not rzs.first():
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print(" --- No rzs, continue")
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continue
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ppl, source_id = get_by_id(row['Person'], Person, first=False)
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print(" +++ ppl=%s, source_id=%s" % (ppl, source_id))
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if not ppl or not ppl.first():
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print(" --- No ppl, continue")
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continue
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with transaction.atomic():
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person = ppl.first()
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research_ranges = add_linked(person, MountainRange, row['MountainRange'])
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ranges_people = [PeopleRange.objects.get_or_create(range_id=r.id, person_id=person.id)[0] for r in research_ranges]
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person.peoplerange_set.set(ranges_people)
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# for person in ppl:
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# research_ranges = add_linked(person, MountainRange, row['MountainRange'])
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# ranges_people = [RangesPeople.objects.get_or_create(range_id=r.id, person_id=person.id)[0] for r in research_ranges]
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# person.rangespeople_set.set(ranges_people)
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# ranges_people = RangesPeople
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# for r in rzs:
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# ranges_people.append(r)
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# person.rangespeople_set.set(ranges_people)
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person.save()
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#print(" *** Saved %s => %s (%s)" % (person, ranges_people, len(ranges_people)))
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count = count + 1
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elif fmt['extension'] == 'geojson':
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ranges_missing = []
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with open(filename, 'rt', encoding='utf-8', errors='ignore') as jsonfile:
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jsondata = json.load(jsonfile)
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if fmt['dataformat'] is DataFormat.RANGE_SHAPES:
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totalrows = len(jsondata['features'])
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for f in jsondata['features']:
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yield count, count / totalrows
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count = count + 1
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p = f['properties']
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rge = MountainRange.objects.filter(gmba_id=p['GMBA_ID']).first()
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if not rge:
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ranges_missing.append(p['GMBA_ID'])
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continue
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rge.name = p['Name']
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for c in ['Country_1', 'Country_2_']:
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if c in p: rge.countries = p[c]
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rge.save()
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print("Warning: %d ranges not found" % len(ranges_missing))
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print("[%s]" % ', '.join(ranges_missing))
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yield None, None
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return count
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