Fix db errors in convert.py
- use print for logger for the time being - replace db.session with obj.save methods - use transaction for no_flush case TODO: change query / filter / filter_by
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PCoder
parent
0b93703886
commit
b628f6621d
1 changed files with 20 additions and 22 deletions
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@ -1,9 +1,11 @@
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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 app.models import *
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from .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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@ -29,7 +31,7 @@ def add_linked(person, field, obj, data):
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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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tgt.save()
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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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@ -53,9 +55,7 @@ def get_total_rows_csv(filename):
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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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p.save()
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# Data update routine
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def refresh_data(filename, fmt=None):
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@ -63,7 +63,7 @@ def refresh_data(filename, fmt=None):
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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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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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@ -76,14 +76,14 @@ def refresh_data(filename, fmt=None):
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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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# # 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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print(msg)
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yield(msg, "error")
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return None
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@ -104,14 +104,14 @@ def refresh_data(filename, fmt=None):
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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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with transaction.atomic():
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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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person.save()
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count = count + 1
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elif fmt['dataformat'] is DataFormat.RESOURCE_DETAIL:
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@ -121,7 +121,7 @@ def refresh_data(filename, fmt=None):
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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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res.save()
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count = count + 1
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elif fmt['dataformat'] is DataFormat.RANGE_DETAIL:
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@ -130,7 +130,7 @@ def refresh_data(filename, fmt=None):
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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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rng.save()
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count = count + 1
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elif fmt['dataformat'] is DataFormat.PERSON_RESOURCE:
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@ -140,7 +140,7 @@ def refresh_data(filename, fmt=None):
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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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person.save()
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count = count + 1
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elif fmt['dataformat'] is DataFormat.PERSON_RANGE:
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@ -150,7 +150,7 @@ def refresh_data(filename, fmt=None):
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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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person.save()
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count = count + 1
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elif fmt['extension'] == 'geojson':
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@ -171,10 +171,8 @@ def refresh_data(filename, fmt=None):
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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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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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