Add convert.py as is from gmba-connect
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PCoder
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gmba_django/convert.py
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gmba_django/convert.py
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import csv, json, re
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from app import app
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from os.path import isfile
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from .models import *
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from .formats import *
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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, field, obj, data):
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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: continue
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tgt = obj.query.filter_by(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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db.session.add(tgt)
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field.append(tgt)
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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.query.filter_by(source_id=rowid)
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if first: return l.first(), rowid
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else: 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.query.all()):
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p.index()
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db.session.add(p)
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if i % 10 == 0: db.session.commit()
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db.session.commit()
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# Data update routine
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def refresh_data(filename, fmt=None):
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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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app.logger.warn(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: 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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app.logger.warn(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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person, source_id = get_by_id(row['ID'], Person)
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if not person:
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person = Person.query.filter_by(first_name=row['First name'], last_name=row['Last name']).first()
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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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# Update data fields
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person.source_id = source_id
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person.title = row['Title']
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person.organisation = row['Organisation English']
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person.country = row['Country']
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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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with db.session.no_autoflush:
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add_linked(person, person.research_methods, Method, row['Methods'])
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add_linked(person, person.research_scales, Scale, row['Scale'])
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add_linked(person, person.research_taxa, Taxon, row['Taxa'])
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add_linked(person, person.research_fields, Field, row['Field of expertise'])
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person.index()
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db.session.add(person)
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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: 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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db.session.add(res)
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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'], Range)
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if not rng: rng = Range(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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db.session.add(rng)
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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(): 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(): continue
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for person in ppl:
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for r in rzs: person.resources.append(r)
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db.session.add(person)
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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'], Range, first=False)
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if not rzs or not rzs.first(): 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(): continue
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for person in ppl:
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for r in rzs: person.ranges.append(r)
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db.session.add(person)
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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 = Range.query.filter_by(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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db.session.add(rge)
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app.logger.info("Warning: %d ranges not found" % len(ranges_missing))
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app.logger.debug("[%s]" % ', '.join(ranges_missing))
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db.session.commit()
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yield None, None
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return count
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