Initial recut of data import
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6162bd984f
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5 changed files with 69 additions and 302 deletions
69
ccdb/utils/data.py
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69
ccdb/utils/data.py
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import sqlite3
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import os
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import json
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from django.conf import settings
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import requests
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import dateutil.parser as dp
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def get_data_sources():
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manifest_url = settings.MANIFEST_URL
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if not manifest_url:
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return None
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data_dir = 'data/'
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if not os.path.exists(data_dir):
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os.makedirs(data_dir)
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_fetch_data(data_dir, manifest_url)
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return {
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'db0': _get_db0(),
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}
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def _fetch_data(data_dir, url):
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manifest = _filename(data_dir, url)
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if not os.path.exists(manifest):
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_write_url(url, manifest)
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with open(manifest) as data:
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d = json.load(data)
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for f in d['files']:
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p = _filename(data_dir, f)
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if not os.path.exists(p):
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_write_url(f, p)
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def _filename(data_dir, url):
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return ''.join([data_dir, url.split('/')[-1]])
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def _write_url(url, filename):
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r = requests.get(url, stream=True)
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with open(filename, 'wb') as outfile:
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for chunk in r:
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outfile.write(chunk)
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def _get_db0():
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dbfile = 'data/Replica_Hibernators_Back_UAF_Laptop_29_June_2015.sqlite'
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return setup_sqlite(dbfile)
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def dtdt(s):
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"""
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This lets us parse whatever crazy date/time formats that
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come our way (looking at you, MS Access)
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"""
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return dp.parse(s)
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sqlite3.register_converter("dtdt", dtdt)
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def setup_sqlite(dbfile):
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if os.path.exists(dbfile):
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db = sqlite3.connect(dbfile, detect_types=sqlite3.PARSE_DECLTYPES | sqlite3.PARSE_COLNAMES)
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db.row_factory = sqlite3.Row
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return db.cursor()
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else:
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return None
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@ -1,25 +0,0 @@
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import sqlite3
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import os
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import dateutil.parser as dp
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def dtdt(s):
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"""
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This lets us parse whatever crazy date/time formats that
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come our way (looking at you, MS Access)
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"""
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return dp.parse(s)
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sqlite3.register_converter("dtdt", dtdt)
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def setup_sqlite():
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dbfile = 'data/CC_Database_101314.sqlite'
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if os.path.exists(dbfile):
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db = sqlite3.connect(dbfile, detect_types=sqlite3.PARSE_DECLTYPES|sqlite3.PARSE_COLNAMES)
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db.row_factory = sqlite3.Row
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return db.cursor()
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else:
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return None
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import os
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from django.core.management.base import BaseCommand
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from django.db import IntegrityError
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import requests
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from ccdb.utils.data_import import setup_sqlite
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from ccdb.projects.models import Project, Grant, GrantReport
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from ccdb.misc.models import MeasurementUnit, MeasurementType, Container, \
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Material, Color
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from ccdb.locations.models import Region, Site, MunicipalLocation, \
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StudyLocation, StorageLocation
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from ccdb.species.models import Species, CollectionSpecies
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from ccdb.processing.models import ProcessType, Reagent, \
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Flaw as ProcessingFlaw,Processing
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from ccdb.collections_ccdb.models import CollectionType, CollectionMethod, \
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Flaw as CollectionFlaw, ADFGPermit, Collection
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from ccdb.experiments.models import Flaw as ExperimentFlaw, Experiment, \
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ProtocolAttachment, TreatmentType, Treatment, TreatmentReplicate, \
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AliveDeadCount
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class Command(BaseCommand):
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help = 'Imports prior data into the DB'
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def add_arguments(self, parser):
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parser.add_argument('manifest_url', type=str)
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def handle(self, **options):
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_fetch_data(options['manifest_url'], self.stdout.write)
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self.stdout.write('Fetched data')
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_import_admin_data()
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self.stdout.write('Imported data')
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def _fetch_data(url, write):
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data_dir = 'data/'
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r = requests.get(url)
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files = r.json()
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if not os.path.exists(data_dir):
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os.makedirs(data_dir)
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for f in files['files']:
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p = ''.join([data_dir, f.split('/')[-1]])
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if not os.path.exists(p):
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write('Grabbing {}'.format(p))
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r = requests.get(f, stream=True)
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with open(p, 'wb') as out_file:
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for chunk in r:
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out_file.write(chunk)
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def _import_admin_data():
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c = setup_sqlite()
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if c:
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# Projects
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for r in c.execute('SELECT * FROM tbl_lu_projects;'):
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p = Project(id=r[0], name=r[1], code=r[2], iacuc_number=r[3],
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description=r[4], sort_order=r[5])
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p.save()
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# Grants
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for r in c.execute('SELECT * FROM tbl_lu_grants;'):
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g = Grant(id=r[0], title=r[1], code=r[2],
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description=r[3], sort_order=r[4])
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g.save()
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# Project-Grants
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for r in c.execute('SELECT * FROM tbl_hash_project_grants;'):
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p = Project.objects.get(id=r[0])
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g = Grant.objects.get(id=r[1])
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p.grants.add(g)
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p.save()
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# Grant Reports
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q = '''
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SELECT *, report_due_date AS "due_date [dtdt]"
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FROM tbl_lu_grant_reports;
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'''
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for r in c.execute(q):
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# No PK field in Andre's file
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gr = GrantReport(grant_id=r[0], title=r[1], report_type=r[2],
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description=r[3], due_date=r[8], submitted_date=r[5],
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attachment=r[6], sort_order=r[7])
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try:
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gr.save()
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except IntegrityError:
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pass
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# Measurement Units
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for r in c.execute('SELECT * FROM tbl_lu_measurement_units;'):
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mu = MeasurementUnit(id=r[0], name=r[1], code=r[2],
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unit_class=r[3], description=r[4], sort_order=r[5])
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mu.save()
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# Measurement Types
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for r in c.execute('SELECT * FROM tbl_lu_measurement_types;'):
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mt = MeasurementType(id=r[0], name=r[1], code=r[2],
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measurement_type_class=r[3], description=r[4],
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default_measurement_unit_id=r[5], sort_order=r[6])
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mt.save()
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# Materials
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for r in c.execute('SELECT * FROM tbl_lu_materials;'):
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m = Material(id=r[0], name=r[1], code=r[2], material_class=r[3],
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description=r[4], sort_order=r[5])
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m.save()
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# Colors
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for r in c.execute('SELECT * FROM tbl_lu_colors;'):
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cl = Color(id=r[0], name=r[1], code=r[2],
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color_number=r[3], sort_order=r[4])
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cl.save()
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# Containers
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for r in c.execute('SELECT * FROM tbl_lu_containers;'):
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cl = Container(id=r[0], name=r[1], code=r[2], application=r[3],
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color_id=r[4], material_id=r[5], volume=r[6],
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measurement_unit_id=r[7], sort_order=r[8])
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cl.save()
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# Regions
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for r in c.execute('SELECT * FROM tbl_lu_regions;'):
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re = Region(id=r[0], name=r[1], code=r[2], sort_order=r[3])
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re.save()
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# Site
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for r in c.execute('SELECT * FROM tbl_lu_sites;'):
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s = Site(region_id=r[0], id=r[1], name=r[2], code=r[3],
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description=r[4], sort_order=r[5])
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s.save()
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# Municipal Locations
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for r in c.execute('SELECT * FROM tbl_lu_municipal_locations;'):
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ml = MunicipalLocation(id=r[1], name=r[2], code=r[3],
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municipal_location_type=r[4], description=r[5], sort_order=r[6])
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ml.save()
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# Study Locations
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for r in c.execute('SELECT * FROM tbl_lu_study_locations;'):
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sl = StudyLocation(site_id=r[0], id=r[1], name=r[2], code=r[3],
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study_location_type=r[4], treatment_type=r[5],
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municipal_location_id=r[6], collecting_location=r[7],
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description=r[13], sort_order=r[14])
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sl.save()
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# Storage Location
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for r in c.execute('SELECT * FROM tbl_lu_storage_locations;'):
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bldg = "".join(e[0].upper() for e in r[2].split())
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temp_c = '20'
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if r[5]:
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temp_c = r[5]
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freezer = 'No Freezer'
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if r[4]:
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freezer = r[4]
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code = " ".join([bldg, str(temp_c)+'C', str(freezer)])
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sl = StorageLocation(id=r[0], facility=r[1], building=r[2],
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room=r[3], freezer=r[4], temp_c=r[5], code=code,
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description=r[6], sort_order=r[7])
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sl.save()
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# Species
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for r in c.execute('SELECT * FROM tbl_lu_species;'):
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s = Species(id=r[0], common_name=r[1], genus=r[2], species=r[3],
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parasite=r[4], sort_order=r[5])
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s.save()
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# Processing Type
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for r in c.execute('SELECT * FROM tbl_lu_process_types;'):
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pt = ProcessType(id=r[0], name=r[1], code=r[2], description=r[3],
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sort_order=r[4])
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pt.save()
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# Reagent
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for r in c.execute('SELECT * FROM tbl_lu_reagents;'):
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rg = Reagent(id=r[0], name=r[1], code=r[2], reagent_class=r[3],
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sort_order=r[4])
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rg.save()
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# Collection Type
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for r in c.execute('SELECT * FROM tbl_lu_collection_types;'):
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ct = CollectionType(id=r[0], name=r[1], code=r[2], sort_order=r[3])
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ct.save()
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# Collection Method
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for r in c.execute('SELECT * FROM tbl_lu_collection_methods;'):
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cm = CollectionMethod(id=r[0], name=r[1], code=r[2],
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collection_method_class=r[3], sort_order=r[4])
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cm.save()
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# Collection
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for r in c.execute('''
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SELECT *,
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collection_start_date AS "collection_start_date [dtdt]",
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collection_start_time AS "collection_start_time [dtdt]",
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collection_end_date AS "collection_end_date [dtdt]",
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collection_end_time AS "collection_end_time [dtdt]"
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FROM tbl_collections;
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'''):
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if r[14] is not '':
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permit, _ = ADFGPermit.objects.get_or_create(name=r[14])
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else:
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permit = None
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col = Collection(project_id=r[0], id=r[1], study_location_id=r[2],
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collection_type_id=r[3], collection_method_id=r[4],
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number_of_traps=r[5], collection_start_date=r[17],
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collection_start_time=r[18], collection_end_date=r[19],
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collection_end_time=r[20], storage_location_id=r[10],
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specimen_state=r[11], process_type_id=r[12], reagent_id=r[13],
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adfg_permit=permit)
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col.save()
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# Collection Species
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for r in c.execute('SELECT * FROM tbl_hash_collection_species;'):
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# No PK field in Andre's file
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cs = CollectionSpecies(collection_id=r[0], species_id=r[1],
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sex=r[2], count=r[3], count_estimated=r[4])
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try:
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cs.save()
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except IntegrityError:
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pass
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# Experiment
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for r in c.execute('SELECT * FROM tbl_lu_experiments;'):
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e = Experiment(id=r[0], name=r[1], code=r[2],
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description=r[3], sort_order=r[6])
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e.save()
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# Treatment Type
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for r in c.execute('SELECT * FROM tbl_lu_treatment_types;'):
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tt = TreatmentType(experiment_id=r[0], id=r[1], name=r[2], code=r[3],
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treatment_type=r[4], placement=r[5], description=r[6])
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tt.save()
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# Treatment
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for r in c.execute('SELECT * FROM tbl_treatments;'):
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t = Treatment(id=r[0], treatment_type_id=r[1], container_id=r[2],
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study_location_id=r[3], species_id=r[4], sex=r[5])
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t.save()
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# Treatment Replicate
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for r in c.execute('''
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SELECT *, setup_date AS "setup_date [dtdt]"
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FROM tbl_treatment_replicates tr
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LEFT OUTER JOIN tbl_lu_record_flaws f ON f.flawid=tr.flawid;
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'''):
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if r[7]:
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flaw, _ = ExperimentFlaw.objects.get_or_create(name=r[10])
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else:
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flaw = None
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tr = TreatmentReplicate(treatment_id=r[0], id=r[1], name=r[2],
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setup_date=r[13], setup_sample_size=r[5], mass_g=r[6], flaw=flaw)
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tr.save()
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# Alive-Dead Count
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for r in c.execute('''
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SELECT *,
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status_date AS "status_date [dtdt]",
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status_time AS "status_time [dtdt]"
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FROM tbl_alive_dead_counts adc
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LEFT OUTER JOIN tbl_lu_record_flaws f ON f.flawid=adc.flawid;
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'''):
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if r[6]:
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flaw, _ = ExperimentFlaw.objects.get_or_create(name=r[9])
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else:
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flaw = None
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adc = AliveDeadCount(treatment_replicate_id=r[0], id=r[1],
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status_date=r[12], status_time=r[13], count_alive=r[4],
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count_dead=r[5], flaw=flaw)
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adc.save()
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# Experiment-Collection
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for r in c.execute('SELECT * FROM tbl_hash_collection_experiments;'):
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c = Collection.objects.get(id=r[0])
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e = Experiment.objects.get(id=r[1])
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e.collections.add(c)
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e.save()
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